Header list of 1xu0.pdb file
Complete list - r 2 2 Bytes
HEADER MEMBRANE PROTEIN 25-OCT-04 1XU0
TITLE SOLUTION STRUCTURE OF XENOPUS LEAVIS PRION PROTEIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PRION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: GLOBULAR DOMAIN(RESIDUES 98-226);
COMPND 5 SYNONYM: XLPRP;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS;
SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG;
SOURCE 4 ORGANISM_TAXID: 8355;
SOURCE 5 GENE: PRNP;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET
KEYWDS PRION, AMPHIBIAN, POLYMORPHISM, GLYCOPROTEIN, MEMBRANE PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR D.R.PEREZ,K.WUTHRICH
REVDAT 5 02-MAR-22 1XU0 1 REMARK SEQADV
REVDAT 4 24-FEB-09 1XU0 1 VERSN
REVDAT 3 25-JAN-05 1XU0 1 JRNL
REVDAT 2 11-JAN-05 1XU0 1 JRNL AUTHOR
REVDAT 1 04-JAN-05 1XU0 0
JRNL AUTH L.CALZOLAI,D.A.LYSEK,D.R.PEREZ,P.GUNTERT,K.WUTHRICH
JRNL TITL PRION PROTEIN NMR STRUCTURES OF CHICKEN, TURTLE, AND FROG
JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 651 2005
JRNL REFN ISSN 0027-8424
JRNL PMID 15647366
JRNL DOI 10.1073/PNAS.0408939102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 6.01, OPALP
REMARK 3 AUTHORS : GUNTERT, P., MUMENTHALER, C. & WUTHRICH, K.
REMARK 3 (DYANA), R.KORADI,M.BILLITER,P.GUNTERT (OPALP)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 2283 NOE-DERIVED DISTANCE RESTRAINTS.
REMARK 4
REMARK 4 1XU0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-04.
REMARK 100 THE DEPOSITION ID IS D_1000030768.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293.15
REMARK 210 PH : 4.5
REMARK 210 IONIC STRENGTH : 10MM SODIUM ACETAT
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : U-15N, U-13C; 95% H2O, 5% D2O; U
REMARK 210 -15N, U-13C; 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY ALIPHATIC
REMARK 210 REGION; 3D_13C-SEPARATED_NOESY
REMARK 210 AROMATIC REGION
REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CANDID
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-20
REMARK 465 RES C SSSEQI
REMARK 465 GLY A 97
REMARK 465 SER A 98
REMARK 465 GLY A 99
REMARK 465 TYR A 100
REMARK 465 ASN A 101
REMARK 465 LYS A 102
REMARK 465 GLN A 103
REMARK 465 TRP A 104
REMARK 465 LYS A 105
REMARK 465 PRO A 106
REMARK 465 PRO A 107
REMARK 465 LYS A 108
REMARK 465 SER A 109
REMARK 465 LYS A 110
REMARK 465 THR A 111
REMARK 465 ASN A 112
REMARK 465 MET A 113
REMARK 465 LYS A 114
REMARK 465 SER A 115
REMARK 465 VAL A 116
REMARK 465 ALA A 117
REMARK 465 ILE A 118
REMARK 465 GLY A 119
REMARK 465 ALA A 120
REMARK 465 ALA A 121
REMARK 465 ALA A 122
REMARK 465 GLY A 123
REMARK 465 ALA A 124
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 TYR A 153 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 TYR A 162 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 4 TYR A 139 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES
REMARK 500 6 TYR A 139 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 6 VAL A 209 CA - CB - CG2 ANGL. DEV. = 10.3 DEGREES
REMARK 500 10 ARG A 163 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 11 CYS A 218 CA - CB - SG ANGL. DEV. = 6.8 DEGREES
REMARK 500 12 VAL A 209 CA - CB - CG1 ANGL. DEV. = 11.5 DEGREES
REMARK 500 12 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 14 TYR A 162 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 16 ARG A 167 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 16 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 18 VAL A 161 CA - CB - CG2 ANGL. DEV. = 9.3 DEGREES
REMARK 500 19 ASP A 175 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 VAL A 134 -81.02 -122.54
REMARK 500 1 ARG A 136 16.70 52.45
REMARK 500 1 MET A 137 -74.95 20.30
REMARK 500 1 TYR A 139 173.51 -50.79
REMARK 500 1 PHE A 141 162.41 55.33
REMARK 500 1 GLU A 169 -72.48 -101.16
REMARK 500 1 GLU A 170 6.64 53.37
REMARK 500 1 TYR A 171 42.74 -144.32
REMARK 500 1 ILE A 190 -55.38 -130.11
REMARK 500 1 SER A 200 79.29 45.85
REMARK 500 1 GLU A 201 -14.20 71.80
REMARK 500 2 LEU A 130 154.34 65.24
REMARK 500 2 ARG A 136 -10.33 70.25
REMARK 500 2 MET A 137 -69.75 34.95
REMARK 500 2 TYR A 139 175.04 -55.88
REMARK 500 2 GLN A 140 91.44 -67.75
REMARK 500 2 TYR A 166 179.91 52.52
REMARK 500 2 GLU A 169 -78.40 -69.37
REMARK 500 2 GLU A 170 -109.64 -161.59
REMARK 500 2 TYR A 171 52.68 -149.29
REMARK 500 2 ILE A 190 -60.82 -133.45
REMARK 500 2 LYS A 197 68.26 32.35
REMARK 500 2 SER A 200 88.45 44.62
REMARK 500 2 GLU A 201 -42.12 81.96
REMARK 500 3 MET A 129 14.19 -144.63
REMARK 500 3 LEU A 130 168.45 56.91
REMARK 500 3 VAL A 134 -74.29 -108.27
REMARK 500 3 ARG A 136 75.63 -105.57
REMARK 500 3 SER A 138 59.32 28.49
REMARK 500 3 TYR A 139 179.60 -52.15
REMARK 500 3 TYR A 162 64.09 -112.33
REMARK 500 3 TYR A 171 -164.90 -65.31
REMARK 500 3 VAL A 172 172.03 60.41
REMARK 500 3 ILE A 190 -49.03 -136.45
REMARK 500 3 LYS A 197 112.43 53.07
REMARK 500 3 ASN A 198 82.82 -69.80
REMARK 500 3 ASN A 199 -71.97 -137.85
REMARK 500 3 SER A 200 94.83 46.94
REMARK 500 3 GLU A 201 -22.15 74.08
REMARK 500 4 TYR A 128 111.47 67.63
REMARK 500 4 LEU A 130 135.00 77.01
REMARK 500 4 VAL A 134 -66.61 -90.38
REMARK 500 4 ARG A 136 67.18 23.00
REMARK 500 4 PHE A 141 176.25 62.11
REMARK 500 4 ILE A 190 -56.11 -132.52
REMARK 500 4 GLU A 201 -33.77 121.43
REMARK 500 4 GLN A 212 -70.07 -58.99
REMARK 500 5 LEU A 130 137.72 69.71
REMARK 500 5 ASN A 132 176.92 50.37
REMARK 500 5 VAL A 134 -70.85 -129.83
REMARK 500
REMARK 500 THIS ENTRY HAS 208 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ARG A 163 PRO A 164 8 148.12
REMARK 500 TYR A 139 GLN A 140 20 141.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 TYR A 139 0.07 SIDE CHAIN
REMARK 500 1 ARG A 148 0.08 SIDE CHAIN
REMARK 500 1 ARG A 160 0.07 SIDE CHAIN
REMARK 500 3 ARG A 148 0.11 SIDE CHAIN
REMARK 500 3 ARG A 215 0.08 SIDE CHAIN
REMARK 500 3 ARG A 223 0.12 SIDE CHAIN
REMARK 500 4 TYR A 139 0.13 SIDE CHAIN
REMARK 500 4 TYR A 154 0.07 SIDE CHAIN
REMARK 500 4 ARG A 163 0.09 SIDE CHAIN
REMARK 500 4 ARG A 167 0.08 SIDE CHAIN
REMARK 500 5 TYR A 139 0.06 SIDE CHAIN
REMARK 500 5 ARG A 215 0.09 SIDE CHAIN
REMARK 500 5 ARG A 223 0.08 SIDE CHAIN
REMARK 500 6 TYR A 149 0.12 SIDE CHAIN
REMARK 500 6 TYR A 171 0.09 SIDE CHAIN
REMARK 500 7 TYR A 128 0.10 SIDE CHAIN
REMARK 500 7 TYR A 150 0.09 SIDE CHAIN
REMARK 500 7 TYR A 162 0.08 SIDE CHAIN
REMARK 500 7 ARG A 215 0.08 SIDE CHAIN
REMARK 500 8 TYR A 149 0.08 SIDE CHAIN
REMARK 500 8 ARG A 167 0.07 SIDE CHAIN
REMARK 500 8 TYR A 189 0.06 SIDE CHAIN
REMARK 500 8 ARG A 215 0.09 SIDE CHAIN
REMARK 500 9 ARG A 160 0.09 SIDE CHAIN
REMARK 500 9 TYR A 162 0.07 SIDE CHAIN
REMARK 500 9 ARG A 167 0.08 SIDE CHAIN
REMARK 500 9 ARG A 223 0.08 SIDE CHAIN
REMARK 500 10 ARG A 163 0.11 SIDE CHAIN
REMARK 500 10 TYR A 189 0.07 SIDE CHAIN
REMARK 500 11 TYR A 139 0.14 SIDE CHAIN
REMARK 500 11 TYR A 222 0.09 SIDE CHAIN
REMARK 500 12 TYR A 139 0.08 SIDE CHAIN
REMARK 500 12 ARG A 163 0.10 SIDE CHAIN
REMARK 500 12 TYR A 166 0.11 SIDE CHAIN
REMARK 500 13 ARG A 136 0.09 SIDE CHAIN
REMARK 500 13 ARG A 148 0.09 SIDE CHAIN
REMARK 500 13 ARG A 160 0.10 SIDE CHAIN
REMARK 500 13 TYR A 162 0.09 SIDE CHAIN
REMARK 500 13 ARG A 176 0.08 SIDE CHAIN
REMARK 500 14 TYR A 171 0.08 SIDE CHAIN
REMARK 500 15 TYR A 139 0.08 SIDE CHAIN
REMARK 500 15 TYR A 149 0.07 SIDE CHAIN
REMARK 500 15 TYR A 153 0.10 SIDE CHAIN
REMARK 500 15 TYR A 162 0.07 SIDE CHAIN
REMARK 500 15 TYR A 222 0.12 SIDE CHAIN
REMARK 500 16 TYR A 139 0.09 SIDE CHAIN
REMARK 500 16 TYR A 149 0.09 SIDE CHAIN
REMARK 500 16 ARG A 176 0.11 SIDE CHAIN
REMARK 500 16 TYR A 189 0.09 SIDE CHAIN
REMARK 500 16 ARG A 224 0.10 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 61 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1U3M RELATED DB: PDB
REMARK 900 PRION PROTEIN FROM CHICKEN
REMARK 900 RELATED ID: 1U5L RELATED DB: PDB
REMARK 900 PRION PROTEIN FROM TURTLE
DBREF 1XU0 A 98 226 UNP Q5S1W7 Q5S1W7_XENLA 43 171
SEQADV 1XU0 GLY A 97 UNP Q5S1W7 CLONING ARTIFACT
SEQRES 1 A 130 GLY SER GLY TYR ASN LYS GLN TRP LYS PRO PRO LYS SER
SEQRES 2 A 130 LYS THR ASN MET LYS SER VAL ALA ILE GLY ALA ALA ALA
SEQRES 3 A 130 GLY ALA ILE GLY GLY TYR MET LEU GLY ASN ALA VAL GLY
SEQRES 4 A 130 ARG MET SER TYR GLN PHE ASN ASN PRO MET GLU SER ARG
SEQRES 5 A 130 TYR TYR ASN ASP TYR TYR ASN GLN MET PRO ASN ARG VAL
SEQRES 6 A 130 TYR ARG PRO MET TYR ARG GLY GLU GLU TYR VAL SER GLU
SEQRES 7 A 130 ASP ARG PHE VAL ARG ASP CYS TYR ASN MET SER VAL THR
SEQRES 8 A 130 GLU TYR ILE ILE LYS PRO ALA GLU GLY LYS ASN ASN SER
SEQRES 9 A 130 GLU LEU ASN GLN LEU ASP THR THR VAL LYS SER GLN ILE
SEQRES 10 A 130 ILE ARG GLU MET CYS ILE THR GLU TYR ARG ARG GLY SER
HELIX 1 1 ASN A 143 TYR A 153 1 11
HELIX 2 2 TYR A 154 GLN A 156 5 3
HELIX 3 3 SER A 173 TYR A 189 1 17
HELIX 4 4 ILE A 190 GLY A 196 5 7
HELIX 5 5 LEU A 202 GLY A 225 1 24
SHEET 1 A 2 GLY A 127 ALA A 133 0
SHEET 2 A 2 ARG A 160 MET A 165 -1 O ARG A 163 N MET A 129
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - r 2 2 Bytes