Header list of 1s6n.pdb file
Complete list - r 25 2 Bytes
HEADER VIRAL PROTEIN 26-JAN-04 1S6N
TITLE NMR STRUCTURE OF DOMAIN III OF THE WEST NILE VIRUS ENVELOPE PROTEIN,
TITLE 2 STRAIN 385-99
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DOMAIN III;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: WEST NILE VIRUS;
SOURCE 3 ORGANISM_TAXID: 307044;
SOURCE 4 STRAIN: 385-99;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C2X;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMAL C2X
KEYWDS BETA BARREL, FLAVIVIRUS, VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR D.E.VOLK,D.W.BEASLEY,D.A.KALLICK,M.R.HOLBROOK,A.D.BARRETT,
AUTHOR 2 D.G.GORENSTEIN
REVDAT 4 13-JUL-11 1S6N 1 VERSN
REVDAT 3 24-FEB-09 1S6N 1 VERSN
REVDAT 2 28-SEP-04 1S6N 1 JRNL
REVDAT 1 06-JUL-04 1S6N 0
JRNL AUTH D.E.VOLK,D.W.BEASLEY,D.A.KALLICK,M.R.HOLBROOK,A.D.BARRETT,
JRNL AUTH 2 D.G.GORENSTEIN
JRNL TITL SOLUTION STRUCTURE AND ANTIBODY BINDING STUDIES OF THE
JRNL TITL 2 ENVELOPE PROTEIN DOMAIN III FROM THE NEW YORK STRAIN OF WEST
JRNL TITL 3 NILE VIRUS
JRNL REF J.BIOL.CHEM. V. 279 38755 2004
JRNL REFN ISSN 0021-9258
JRNL PMID 15190071
JRNL DOI 10.1074/JBC.M402385200
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.E.VOLK,D.A.KALLICK,M.R.HOLBROOK,D.W.C.BEASLEY,
REMARK 1 AUTH 2 A.D.T.BARRETT,D.G.GORENSTEIN
REMARK 1 TITL LETTER TO THE EDITOR: 1H, 13C, AND 15N RESONANCE ASSIGNMENTS
REMARK 1 TITL 2 FOR DOMAIN III OF THE WEST NILE VIRUS ENVELOPE PROTEIN
REMARK 1 REF TO BE PUBLISHED
REMARK 1 REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 6
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,
REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1S6N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-04.
REMARK 100 THE RCSB ID CODE IS RCSB021433.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 50MM PHOSPHATE, 100MM NACL, 10MM
REMARK 210 NAN3
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.7MM WND3 PROTEIN, 50MM K2HPO4,
REMARK 210 100MM NACL, 10MM NAN3, 0.1MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_ 13C-
REMARK 210 SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1B, SANE 1.0, FELIX 98,
REMARK 210 AMBER 6
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: CHEMICAL SHIFTS WERE DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY.
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 HG SER A 50 OD1 ASP A 57 1.31
REMARK 500 OD1 ASP A 90 HG SER A 111 1.32
REMARK 500 HG1 THR A 31 OE1 GLU A 83 1.33
REMARK 500 OD2 ASP A 90 HG SER A 112 1.38
REMARK 500 HH TYR A 38 O ASP A 42 1.51
REMARK 500 HG SER A 51 O GLU A 85 1.54
REMARK 500 HG SER A 2 O PRO A 60 1.56
REMARK 500 O LEU A 58 HG1 THR A 59 1.59
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 63 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 2 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 3 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 3 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 3 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 4 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 5 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 5 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 6 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 6 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 7 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 8 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 8 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 9 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 10 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 10 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 11 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 11 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES
REMARK 500 12 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 12 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 13 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 14 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 14 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 15 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 15 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.2 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 THR A 9 62.11 -68.40
REMARK 500 1 SER A 15 -44.91 -167.27
REMARK 500 1 LYS A 16 -76.09 61.99
REMARK 500 1 ALA A 17 77.06 -102.49
REMARK 500 1 PRO A 44 95.79 -55.11
REMARK 500 1 SER A 54 27.99 -152.93
REMARK 500 1 LEU A 55 17.66 55.47
REMARK 500 1 ASN A 56 52.15 -68.37
REMARK 500 1 ALA A 76 14.31 -66.35
REMARK 500 1 ASN A 77 16.65 -62.22
REMARK 500 1 PRO A 87 167.66 -47.40
REMARK 500 1 SER A 109 70.68 52.41
REMARK 500 2 SER A 15 -44.57 -160.03
REMARK 500 2 LYS A 16 -70.62 64.46
REMARK 500 2 ALA A 17 78.60 -100.81
REMARK 500 2 THR A 39 32.21 -72.72
REMARK 500 2 PRO A 44 87.91 -54.69
REMARK 500 2 SER A 54 36.05 -155.32
REMARK 500 2 LEU A 55 10.03 58.17
REMARK 500 2 ASN A 56 46.28 -68.78
REMARK 500 2 THR A 75 0.66 -63.68
REMARK 500 2 ASN A 77 18.26 -61.63
REMARK 500 2 PRO A 87 150.89 -45.76
REMARK 500 2 SER A 109 -0.22 119.68
REMARK 500 2 SER A 111 -154.77 -88.32
REMARK 500 3 THR A 9 68.96 -62.82
REMARK 500 3 SER A 15 -22.49 -151.14
REMARK 500 3 LYS A 16 -62.41 56.58
REMARK 500 3 PRO A 44 109.01 -51.94
REMARK 500 3 SER A 54 30.84 -154.78
REMARK 500 3 ASN A 56 46.48 -69.52
REMARK 500 3 ALA A 76 12.82 -67.07
REMARK 500 3 ASN A 77 18.04 -65.38
REMARK 500 4 THR A 9 72.57 -67.52
REMARK 500 4 SER A 15 -21.90 -141.00
REMARK 500 4 LYS A 16 -77.75 45.36
REMARK 500 4 PRO A 44 99.18 -50.17
REMARK 500 4 SER A 54 34.75 -154.04
REMARK 500 4 LEU A 55 12.77 57.71
REMARK 500 4 ASN A 56 45.83 -67.01
REMARK 500 4 VAL A 71 89.65 -69.11
REMARK 500 4 ALA A 76 12.80 -65.04
REMARK 500 4 ASN A 77 13.46 -62.75
REMARK 500 4 SER A 109 84.60 59.39
REMARK 500 5 SER A 2 -178.96 -69.05
REMARK 500 5 SER A 15 -3.22 -150.42
REMARK 500 5 LYS A 16 -75.95 53.98
REMARK 500 5 THR A 39 43.33 -77.43
REMARK 500 5 PRO A 44 107.00 -48.04
REMARK 500 5 SER A 54 30.84 -152.17
REMARK 500
REMARK 500 THIS ENTRY HAS 162 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 LYS A 79 VAL A 80 2 -148.60
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 2 ARG A 63 0.13 SIDE CHAIN
REMARK 500 2 ARG A 97 0.09 SIDE CHAIN
REMARK 500 5 TYR A 92 0.07 SIDE CHAIN
REMARK 500 9 ARG A 63 0.08 SIDE CHAIN
REMARK 500 9 TYR A 92 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES 1-5 AND 113-115 ARE NOT IN THE NATIVE SEQUENCE.
REMARK 999 THEY WERE ADDED TO INCREASE SOLUBILITY.
DBREF 1S6N A 6 112 UNP Q913C7 Q913C7_WNV 297 403
SEQADV 1S6N ILE A 1 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N SER A 2 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N GLU A 3 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N PHE A 4 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N GLN A 5 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N ILE A 113 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N GLY A 114 UNP Q913C7 SEE REMARK 999
SEQADV 1S6N LYS A 115 UNP Q913C7 SEE REMARK 999
SEQRES 1 A 115 ILE SER GLU PHE GLN LEU LYS GLY THR THR TYR GLY VAL
SEQRES 2 A 115 CYS SER LYS ALA PHE LYS PHE LEU GLY THR PRO ALA ASP
SEQRES 3 A 115 THR GLY HIS GLY THR VAL VAL LEU GLU LEU GLN TYR THR
SEQRES 4 A 115 GLY THR ASP GLY PRO CYS LYS VAL PRO ILE SER SER VAL
SEQRES 5 A 115 ALA SER LEU ASN ASP LEU THR PRO VAL GLY ARG LEU VAL
SEQRES 6 A 115 THR VAL ASN PRO PHE VAL SER VAL ALA THR ALA ASN ALA
SEQRES 7 A 115 LYS VAL LEU ILE GLU LEU GLU PRO PRO PHE GLY ASP SER
SEQRES 8 A 115 TYR ILE VAL VAL GLY ARG GLY GLU GLN GLN ILE ASN HIS
SEQRES 9 A 115 HIS TRP HIS LYS SER GLY SER SER ILE GLY LYS
SHEET 1 A 4 PHE A 18 ASP A 26 0
SHEET 2 A 4 VAL A 32 TYR A 38 -1 O GLU A 35 N GLY A 22
SHEET 3 A 4 LYS A 79 GLU A 85 -1 O ILE A 82 N LEU A 34
SHEET 4 A 4 ARG A 63 LEU A 64 -1 N ARG A 63 O GLU A 85
SHEET 1 B 3 ILE A 49 VAL A 52 0
SHEET 2 B 3 GLY A 89 ARG A 97 -1 O TYR A 92 N VAL A 52
SHEET 3 B 3 GLN A 100 LYS A 108 -1 O HIS A 104 N ILE A 93
SSBOND 1 CYS A 14 CYS A 45 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 - r 25 2 Bytes