Header list of 1y16.pdb file
Complete list - v 10 2 Bytes
HEADER UNKNOWN FUNCTION 17-NOV-04 1Y16
TITLE MOUSE PRION PROTEIN WITH MUTATIONS S170N AND N174T
CAVEAT 1Y16 CHIRALITY ERROR AT THE CA CENTER OF ARG A 151 (MODEL 20)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MAJOR PRION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN;
COMPND 5 SYNONYM: PRP, PRP27-30, PRP33-35C;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
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 PROTEIN, PRP, PRNP, TSE, CWD, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR A.D.GOSSERT,S.BONJOUR,D.A.LYSEK,F.FIORITO,K.WUTHRICH
REVDAT 3 10-NOV-21 1Y16 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1Y16 1 VERSN
REVDAT 1 25-JAN-05 1Y16 0
JRNL AUTH A.D.GOSSERT,S.BONJOUR,D.A.LYSEK,F.FIORITO,K.WUTHRICH
JRNL TITL PRION PROTEIN NMR STRUCTURES OF ELK AND OF MOUSE/ELK HYBRIDS
JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 646 2005
JRNL REFN ISSN 0027-8424
JRNL PMID 15647363
JRNL DOI 10.1073/PNAS.0409008102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 6.2, CANDID 1.0
REMARK 3 AUTHORS : GUENTERT (DYANA), HERRMANN (CANDID)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS ALSO REFINED WITH
REMARK 3 ATNOS VERSION 1.0 (AUTHOR: HERRMANN)
REMARK 4
REMARK 4 1Y16 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000030985.
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 : 10
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM MPRP(121-213) S170N,N174T U
REMARK 210 -15N,13C;10MM ACETATE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 900 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AVANCE
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 : 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D
REMARK 210 HETERONUCLEAR 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 2 CYS A 179 CA - CB - SG ANGL. DEV. = 6.8 DEGREES
REMARK 500 2 TYR A 226 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 4 VAL A 203 CA - CB - CG2 ANGL. DEV. = 9.6 DEGREES
REMARK 500 4 TYR A 226 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 5 TYR A 226 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES
REMARK 500 6 CYS A 179 CA - CB - SG ANGL. DEV. = 7.1 DEGREES
REMARK 500 8 CYS A 179 CA - CB - SG ANGL. DEV. = 9.1 DEGREES
REMARK 500 9 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 9 CYS A 179 CA - CB - SG ANGL. DEV. = 6.9 DEGREES
REMARK 500 10 CYS A 179 CA - CB - SG ANGL. DEV. = 7.3 DEGREES
REMARK 500 11 VAL A 203 CA - CB - CG2 ANGL. DEV. = 10.5 DEGREES
REMARK 500 12 TYR A 157 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 15 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 15 CYS A 179 CA - CB - SG ANGL. DEV. = 7.2 DEGREES
REMARK 500 15 VAL A 203 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES
REMARK 500 16 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 17 CYS A 179 CA - CB - SG ANGL. DEV. = 9.0 DEGREES
REMARK 500 20 ARG A 151 CD - NE - CZ ANGL. DEV. = 10.4 DEGREES
REMARK 500 20 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 20 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ALA A 133 152.74 154.93
REMARK 500 1 MET A 134 -159.51 -142.18
REMARK 500 1 ASN A 170 -11.88 63.63
REMARK 500 1 VAL A 189 -76.11 -88.80
REMARK 500 1 THR A 193 -59.93 82.53
REMARK 500 1 LYS A 220 -73.22 -92.02
REMARK 500 1 ARG A 229 -87.18 -141.28
REMARK 500 1 SER A 231 50.24 -148.31
REMARK 500 2 SER A 132 -66.08 24.01
REMARK 500 2 ALA A 133 118.39 -177.31
REMARK 500 2 GLU A 152 -71.45 -90.25
REMARK 500 2 ASP A 167 32.73 -68.11
REMARK 500 2 GLN A 168 -0.23 -143.61
REMARK 500 2 VAL A 189 -75.86 -108.50
REMARK 500 2 THR A 193 -76.80 -142.20
REMARK 500 2 LYS A 220 -72.31 -109.64
REMARK 500 2 ARG A 229 -105.79 -139.48
REMARK 500 3 SER A 132 -48.82 -140.10
REMARK 500 3 ALA A 133 121.51 154.52
REMARK 500 3 SER A 135 -154.70 -112.21
REMARK 500 3 ASP A 167 83.28 -62.60
REMARK 500 3 GLN A 168 -32.40 160.77
REMARK 500 3 VAL A 189 -64.41 -126.10
REMARK 500 3 THR A 193 -96.01 -97.19
REMARK 500 3 LYS A 220 -74.07 -87.03
REMARK 500 3 ARG A 229 -105.35 -144.34
REMARK 500 4 LEU A 125 78.69 51.95
REMARK 500 4 SER A 132 -16.54 -43.85
REMARK 500 4 ALA A 133 150.04 96.05
REMARK 500 4 ASP A 167 82.08 -57.81
REMARK 500 4 GLN A 168 -39.02 155.11
REMARK 500 4 THR A 188 4.38 -65.82
REMARK 500 4 VAL A 189 -64.95 -130.29
REMARK 500 4 THR A 193 -71.34 -156.80
REMARK 500 4 LYS A 194 39.85 -140.77
REMARK 500 4 ASN A 197 116.47 -161.18
REMARK 500 4 LYS A 220 -70.94 -89.20
REMARK 500 4 TYR A 226 -53.50 -135.67
REMARK 500 4 ARG A 229 -100.68 -141.61
REMARK 500 4 SER A 231 58.38 -117.75
REMARK 500 5 LEU A 125 89.17 56.47
REMARK 500 5 ALA A 133 132.67 154.58
REMARK 500 5 ASP A 167 31.01 -63.72
REMARK 500 5 GLN A 168 -25.44 -152.75
REMARK 500 5 VAL A 189 -80.49 -118.11
REMARK 500 5 LYS A 220 -66.20 -95.41
REMARK 500 5 SER A 222 -70.25 -68.67
REMARK 500 5 TYR A 226 -55.99 -127.80
REMARK 500 5 ARG A 229 -94.24 -147.13
REMARK 500 6 ALA A 133 136.99 153.94
REMARK 500
REMARK 500 THIS ENTRY HAS 178 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 SER A 231 SER A 232 1 -145.21
REMARK 500 GLU A 196 ASN A 197 3 133.70
REMARK 500 ARG A 230 SER A 231 5 147.65
REMARK 500 ARG A 230 SER A 231 13 139.61
REMARK 500 ASN A 171 GLN A 172 15 146.14
REMARK 500 PRO A 137 MET A 138 19 148.61
REMARK 500 SER A 231 SER A 232 20 -148.07
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 149 0.06 SIDE CHAIN
REMARK 500 1 TYR A 150 0.07 SIDE CHAIN
REMARK 500 2 TYR A 218 0.10 SIDE CHAIN
REMARK 500 2 ARG A 229 0.09 SIDE CHAIN
REMARK 500 3 TYR A 225 0.07 SIDE CHAIN
REMARK 500 3 ARG A 229 0.08 SIDE CHAIN
REMARK 500 5 ARG A 151 0.09 SIDE CHAIN
REMARK 500 5 TYR A 162 0.07 SIDE CHAIN
REMARK 500 5 ARG A 208 0.10 SIDE CHAIN
REMARK 500 5 TYR A 226 0.08 SIDE CHAIN
REMARK 500 5 ARG A 229 0.13 SIDE CHAIN
REMARK 500 6 PHE A 175 0.13 SIDE CHAIN
REMARK 500 6 ARG A 229 0.10 SIDE CHAIN
REMARK 500 7 ARG A 156 0.12 SIDE CHAIN
REMARK 500 7 TYR A 157 0.08 SIDE CHAIN
REMARK 500 8 TYR A 149 0.09 SIDE CHAIN
REMARK 500 8 ARG A 156 0.08 SIDE CHAIN
REMARK 500 8 TYR A 226 0.09 SIDE CHAIN
REMARK 500 8 ARG A 229 0.14 SIDE CHAIN
REMARK 500 9 ARG A 164 0.17 SIDE CHAIN
REMARK 500 10 TYR A 150 0.07 SIDE CHAIN
REMARK 500 11 ARG A 151 0.08 SIDE CHAIN
REMARK 500 11 TYR A 163 0.08 SIDE CHAIN
REMARK 500 12 TYR A 155 0.07 SIDE CHAIN
REMARK 500 12 TYR A 157 0.08 SIDE CHAIN
REMARK 500 13 TYR A 163 0.08 SIDE CHAIN
REMARK 500 13 ARG A 230 0.11 SIDE CHAIN
REMARK 500 14 ARG A 208 0.12 SIDE CHAIN
REMARK 500 15 TYR A 149 0.09 SIDE CHAIN
REMARK 500 15 TYR A 163 0.09 SIDE CHAIN
REMARK 500 15 TYR A 169 0.11 SIDE CHAIN
REMARK 500 16 ARG A 208 0.09 SIDE CHAIN
REMARK 500 16 TYR A 226 0.08 SIDE CHAIN
REMARK 500 17 ARG A 148 0.11 SIDE CHAIN
REMARK 500 17 TYR A 226 0.07 SIDE CHAIN
REMARK 500 18 TYR A 157 0.08 SIDE CHAIN
REMARK 500 18 ARG A 208 0.10 SIDE CHAIN
REMARK 500 19 TYR A 149 0.13 SIDE CHAIN
REMARK 500 19 ARG A 208 0.10 SIDE CHAIN
REMARK 500 19 ARG A 229 0.08 SIDE CHAIN
REMARK 500 20 ARG A 156 0.09 SIDE CHAIN
REMARK 500 20 TYR A 157 0.07 SIDE CHAIN
REMARK 500 20 TYR A 169 0.08 SIDE CHAIN
REMARK 500 20 ARG A 208 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1XYX RELATED DB: PDB
REMARK 900 MOUSE PRION PROTEIN FRAGMENT 121-231
REMARK 900 RELATED ID: 1XYW RELATED DB: PDB
REMARK 900 ELK PRION PROTEIN FRAGMENT 121-231
REMARK 900 RELATED ID: 1Y15 RELATED DB: PDB
REMARK 900 MOUSE PRION PROTEIN WITH MUTATION N174T
DBREF 1Y16 A 121 232 UNP P04925 PRIO_MOUSE 120 231
SEQADV 1Y16 ASN A 170 UNP P04925 SER 169 ENGINEERED MUTATION
SEQADV 1Y16 THR A 174 UNP P04925 ASN 173 ENGINEERED MUTATION
SEQRES 1 A 112 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA
SEQRES 2 A 112 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU
SEQRES 3 A 112 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN
SEQRES 4 A 112 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR ASN ASN GLN
SEQRES 5 A 112 ASN THR PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS
SEQRES 6 A 112 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE
SEQRES 7 A 112 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU
SEQRES 8 A 112 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA
SEQRES 9 A 112 TYR TYR ASP GLY ARG ARG SER SER
HELIX 1 1 ASN A 143 MET A 154 1 12
HELIX 2 2 TYR A 155 TYR A 157 5 3
HELIX 3 3 PRO A 165 TYR A 169 5 5
HELIX 4 4 ASN A 171 THR A 190 1 20
HELIX 5 5 THR A 199 TYR A 225 1 27
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
SSBOND 1 CYS A 179 CYS A 214 1555 1555 2.04
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 - v 10 2 Bytes