Header list of 1xyj.pdb file
Complete list - r 2 2 Bytes
HEADER UNKNOWN FUNCTION 10-NOV-04 1XYJ
TITLE NMR STRUCTURE OF THE CAT PRION PROTEIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PRION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 121-231;
COMPND 5 SYNONYM: CAT PRION PROTEIN;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: FELIS CATUS;
SOURCE 3 ORGANISM_COMMON: DOMESTIC CAT;
SOURCE 4 ORGANISM_TAXID: 9685;
SOURCE 5 GENE: PRNP;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS PRION, TSE, PRP, PRNP, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR D.A.LYSEK,C.SCHORN,L.G.NIVON,V.ESTEVE-MOYA,B.CHRISTEN,L.CALZOLAI,
AUTHOR 2 C.VON SCHROETTER,F.FIORITO,T.HERRMANN,P.GUNTERT
REVDAT 5 02-MAR-22 1XYJ 1 REMARK
REVDAT 4 24-FEB-09 1XYJ 1 VERSN
REVDAT 3 25-JAN-05 1XYJ 1 JRNL
REVDAT 2 11-JAN-05 1XYJ 1 AUTHOR JRNL
REVDAT 1 04-JAN-05 1XYJ 0
JRNL AUTH D.A.LYSEK,C.SCHORN,L.G.NIVON,V.ESTEVE-MOYA,B.CHRISTEN,
JRNL AUTH 2 L.CALZOLAI,C.VON SCHROETTER,F.FIORITO,T.HERRMANN,P.GUNTERT,
JRNL AUTH 3 K.WUTHRICH
JRNL TITL PRION PROTEIN NMR STRUCTURES OF CATS, DOGS, PIGS, AND SHEEP
JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 640 2005
JRNL REFN ISSN 0027-8424
JRNL PMID 15647367
JRNL DOI 10.1073/PNAS.0408937102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 6.2, CANDID 1.0
REMARK 3 AUTHORS : GNTERT (DYANA), HERRMANN (CANDID)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1XYJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000030910.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 4.5
REMARK 210 IONIC STRENGTH : 10MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM FPRP U-15N, 13C; 10MM
REMARK 210 ACETATE BUFFER, PH 4.5
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
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: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D
REMARK 210 TECHNIQUES.
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 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 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 2 VAL A 184 CA - CB - CG1 ANGL. DEV. = 9.0 DEGREES
REMARK 500 3 VAL A 184 CA - CB - CG2 ANGL. DEV. = 12.0 DEGREES
REMARK 500 3 ARG A 228 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 4 VAL A 180 CA - CB - CG2 ANGL. DEV. = 9.2 DEGREES
REMARK 500 4 VAL A 209 CA - CB - CG2 ANGL. DEV. = 9.3 DEGREES
REMARK 500 5 VAL A 184 CA - CB - CG2 ANGL. DEV. = 11.6 DEGREES
REMARK 500 6 VAL A 184 CA - CB - CG2 ANGL. DEV. = 11.6 DEGREES
REMARK 500 7 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 7 TYR A 157 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES
REMARK 500 7 CYS A 179 CA - CB - SG ANGL. DEV. = 6.9 DEGREES
REMARK 500 9 ARG A 228 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 10 PHE A 141 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 10 VAL A 184 CA - CB - CG2 ANGL. DEV. = 12.4 DEGREES
REMARK 500 10 VAL A 209 CA - CB - CG2 ANGL. DEV. = 10.6 DEGREES
REMARK 500 11 VAL A 180 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES
REMARK 500 11 VAL A 184 CA - CB - CG2 ANGL. DEV. = 12.2 DEGREES
REMARK 500 14 VAL A 180 CA - CB - CG2 ANGL. DEV. = 11.3 DEGREES
REMARK 500 14 VAL A 184 CA - CB - CG2 ANGL. DEV. = 10.4 DEGREES
REMARK 500 16 ARG A 148 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES
REMARK 500 16 VAL A 184 CA - CB - CG2 ANGL. DEV. = 12.4 DEGREES
REMARK 500 17 VAL A 180 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES
REMARK 500 18 VAL A 184 CA - CB - CG2 ANGL. DEV. = 12.8 DEGREES
REMARK 500 19 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 20 VAL A 180 CA - CB - CG2 ANGL. DEV. = 9.5 DEGREES
REMARK 500 20 VAL A 184 CA - CB - CG2 ANGL. DEV. = 10.9 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 122 -169.55 -121.52
REMARK 500 1 ALA A 133 125.58 159.35
REMARK 500 1 MET A 134 122.43 -172.43
REMARK 500 1 ARG A 136 71.69 24.55
REMARK 500 1 LEU A 138 89.27 55.40
REMARK 500 1 HIS A 140 83.64 -59.16
REMARK 500 1 ASP A 144 -71.78 -92.44
REMARK 500 1 ASP A 147 -71.03 -88.50
REMARK 500 1 ARG A 156 24.11 -79.84
REMARK 500 1 GLN A 168 -177.51 59.01
REMARK 500 1 TYR A 169 70.07 49.29
REMARK 500 1 CYS A 179 -23.45 -141.97
REMARK 500 1 GLN A 186 7.34 -69.05
REMARK 500 1 PHE A 198 85.71 39.85
REMARK 500 1 ARG A 228 -103.68 -88.92
REMARK 500 1 ARG A 229 143.45 95.60
REMARK 500 1 ALA A 230 77.73 47.97
REMARK 500 2 LEU A 125 1.01 56.83
REMARK 500 2 ALA A 133 111.36 171.76
REMARK 500 2 ARG A 136 73.59 31.69
REMARK 500 2 LEU A 138 90.55 58.65
REMARK 500 2 ASP A 144 -9.09 -58.61
REMARK 500 2 MET A 154 0.47 -59.23
REMARK 500 2 GLN A 160 -148.87 -136.77
REMARK 500 2 VAL A 166 37.54 36.37
REMARK 500 2 TYR A 169 20.18 -157.57
REMARK 500 2 CYS A 179 -52.54 -164.01
REMARK 500 2 GLN A 219 -65.23 -120.17
REMARK 500 2 GLN A 227 -62.22 -151.89
REMARK 500 2 ARG A 229 71.61 34.89
REMARK 500 2 ALA A 230 45.37 -80.39
REMARK 500 3 ALA A 133 87.19 154.58
REMARK 500 3 ARG A 136 80.33 34.98
REMARK 500 3 LEU A 138 134.43 55.05
REMARK 500 3 ASP A 144 -60.61 -120.03
REMARK 500 3 GLN A 168 -166.76 59.52
REMARK 500 3 SER A 170 -132.93 -133.59
REMARK 500 3 ASN A 171 -105.75 -142.08
REMARK 500 3 GLN A 172 -36.07 -131.21
REMARK 500 3 VAL A 176 -70.74 -80.59
REMARK 500 3 ASP A 178 -72.07 62.37
REMARK 500 3 ARG A 228 116.81 -164.38
REMARK 500 3 ARG A 229 -174.91 -68.58
REMARK 500 3 ALA A 230 51.88 71.72
REMARK 500 4 ALA A 133 79.56 -175.46
REMARK 500 4 SER A 135 -173.11 -178.23
REMARK 500 4 ARG A 136 58.14 36.76
REMARK 500 4 LEU A 138 88.61 52.51
REMARK 500 4 ASN A 143 -173.16 -68.19
REMARK 500 4 ASP A 144 -73.29 -120.84
REMARK 500
REMARK 500 THIS ENTRY HAS 292 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 TYR A 163 ARG A 164 3 146.38
REMARK 500 HIS A 177 ASP A 178 3 -147.62
REMARK 500 GLY A 142 ASN A 143 4 147.09
REMARK 500 ASN A 171 GLN A 172 5 147.86
REMARK 500 HIS A 177 ASP A 178 15 -147.90
REMARK 500 GLU A 196 ASN A 197 17 142.05
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 ARG A 148 0.11 SIDE CHAIN
REMARK 500 1 ARG A 151 0.07 SIDE CHAIN
REMARK 500 1 TYR A 157 0.10 SIDE CHAIN
REMARK 500 1 ARG A 228 0.10 SIDE CHAIN
REMARK 500 2 TYR A 145 0.08 SIDE CHAIN
REMARK 500 2 TYR A 157 0.13 SIDE CHAIN
REMARK 500 2 TYR A 226 0.07 SIDE CHAIN
REMARK 500 3 ARG A 151 0.12 SIDE CHAIN
REMARK 500 3 TYR A 163 0.08 SIDE CHAIN
REMARK 500 3 ARG A 229 0.11 SIDE CHAIN
REMARK 500 4 TYR A 128 0.07 SIDE CHAIN
REMARK 500 4 ARG A 136 0.14 SIDE CHAIN
REMARK 500 4 TYR A 157 0.12 SIDE CHAIN
REMARK 500 4 TYR A 218 0.11 SIDE CHAIN
REMARK 500 4 ARG A 228 0.13 SIDE CHAIN
REMARK 500 5 TYR A 128 0.06 SIDE CHAIN
REMARK 500 5 ARG A 156 0.09 SIDE CHAIN
REMARK 500 6 TYR A 157 0.08 SIDE CHAIN
REMARK 500 6 TYR A 169 0.08 SIDE CHAIN
REMARK 500 6 TYR A 225 0.07 SIDE CHAIN
REMARK 500 6 TYR A 226 0.09 SIDE CHAIN
REMARK 500 7 ARG A 136 0.08 SIDE CHAIN
REMARK 500 7 TYR A 149 0.07 SIDE CHAIN
REMARK 500 7 ARG A 228 0.08 SIDE CHAIN
REMARK 500 8 ARG A 136 0.11 SIDE CHAIN
REMARK 500 8 TYR A 163 0.11 SIDE CHAIN
REMARK 500 8 ARG A 164 0.09 SIDE CHAIN
REMARK 500 9 TYR A 128 0.08 SIDE CHAIN
REMARK 500 9 ARG A 151 0.09 SIDE CHAIN
REMARK 500 9 TYR A 155 0.09 SIDE CHAIN
REMARK 500 9 TYR A 162 0.10 SIDE CHAIN
REMARK 500 9 TYR A 226 0.09 SIDE CHAIN
REMARK 500 10 ARG A 136 0.11 SIDE CHAIN
REMARK 500 10 TYR A 157 0.09 SIDE CHAIN
REMARK 500 10 TYR A 163 0.11 SIDE CHAIN
REMARK 500 10 ARG A 229 0.14 SIDE CHAIN
REMARK 500 11 TYR A 169 0.10 SIDE CHAIN
REMARK 500 11 ARG A 228 0.08 SIDE CHAIN
REMARK 500 12 TYR A 150 0.09 SIDE CHAIN
REMARK 500 12 TYR A 225 0.09 SIDE CHAIN
REMARK 500 13 TYR A 149 0.07 SIDE CHAIN
REMARK 500 13 TYR A 162 0.08 SIDE CHAIN
REMARK 500 13 TYR A 218 0.14 SIDE CHAIN
REMARK 500 14 ARG A 151 0.09 SIDE CHAIN
REMARK 500 14 TYR A 157 0.07 SIDE CHAIN
REMARK 500 14 TYR A 163 0.08 SIDE CHAIN
REMARK 500 14 ARG A 229 0.11 SIDE CHAIN
REMARK 500 16 TYR A 155 0.08 SIDE CHAIN
REMARK 500 16 ARG A 164 0.08 SIDE CHAIN
REMARK 500 16 ARG A 229 0.09 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 58 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1XYK RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF THE CANINE PRION PROTEIN
REMARK 900 RELATED ID: 1XYQ RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF THE PIG PRION PROTEIN
DBREF 1XYJ A 121 231 UNP Q5YCW7 Q5YCW7_FELCA 104 214
SEQRES 1 A 111 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA
SEQRES 2 A 111 MET SER ARG PRO LEU ILE HIS PHE GLY ASN ASP TYR GLU
SEQRES 3 A 111 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN
SEQRES 4 A 111 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN
SEQRES 5 A 111 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR VAL ARG
SEQRES 6 A 111 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE
SEQRES 7 A 111 THR GLU THR ASP MET LYS ILE MET GLU ARG VAL VAL GLU
SEQRES 8 A 111 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLU ALA
SEQRES 9 A 111 TYR TYR GLN ARG ARG ALA SER
HELIX 1 1 ASP A 144 GLU A 152 1 9
HELIX 2 2 ASN A 153 TYR A 157 5 5
HELIX 3 3 VAL A 176 THR A 193 1 18
HELIX 4 4 THR A 199 ARG A 228 1 30
SHEET 1 A 2 MET A 129 LEU A 130 0
SHEET 2 A 2 TYR A 162 TYR A 163 -1 O TYR 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