Header list of 1kri.pdb file
Complete list - b 5 2 Bytes
HEADER VIRAL PROTEIN 09-JAN-02 1KRI
TITLE NMR SOLUTION STRUCTURES OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID
TITLE 2 BINDING DOMAIN WITHOUT LIGAND
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VP4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SIALIC ACID BINDING DOMAIN (RESIDUES 46-231);
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RHESUS ROTAVIRUS;
SOURCE 3 ORGANISM_TAXID: 10969;
SOURCE 4 GENE: SEGMENT 4;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 & DL39;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-VP8(46-231)
KEYWDS ROTAVIRUS, VP4, VP8*, SPIKE PROTEIN, OUTER CAPSID, SIALIC ACID,
KEYWDS 2 HEMAGGLUTININ, CELL ATTACHMENT, NEUTRALIZATION ANTIGEN, LECTIN,
KEYWDS 3 GALECTIN FOLD, VIRAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.R.DORMITZER,Z.-Y.J.SUN,G.WAGNER,S.C.HARRISON
REVDAT 4 05-FEB-20 1KRI 1 REMARK
REVDAT 3 27-JAN-16 1KRI 1 REMARK VERSN
REVDAT 2 24-FEB-09 1KRI 1 VERSN
REVDAT 1 27-MAR-02 1KRI 0
JRNL AUTH P.R.DORMITZER,Z.-Y.J.SUN,G.WAGNER,S.C.HARRISON
JRNL TITL THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING DOMAIN HAS A
JRNL TITL 2 GALECTIN FOLD WITH A NOVEL CARBOHYDRATE BINDING SITE
JRNL REF EMBO J. V. 21 885 2002
JRNL REFN ISSN 0261-4189
JRNL PMID 11867517
JRNL DOI 10.1093/EMBOJ/21.5.885
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH P.R.DORMITZER,H.B.GREENBERG,S.C.HARRISON
REMARK 1 TITL PROTEOLYSIS OF MONOMERIC RECOMBINANT ROTAVIRUS VP4 YIELDS AN
REMARK 1 TITL 2 OLIGOMERIC VP5* CORE
REMARK 1 REF J.VIROL. V. 75 7339 2001
REMARK 1 REFN ISSN 0022-538X
REMARK 1 DOI 10.1128/JVI.75.16.7339-7350.2001
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROSA 3.7, CNS 1.0
REMARK 3 AUTHORS : GUNTERT, P., DOTSCH, V., WIDER, G., WUTHRICH, K.
REMARK 3 (PROSA), BRUNGER, A.T., ADAMS, P.D., CLORE, G.M.,
REMARK 3 DELANO, W.L., GROS, P., GROSSE-KUNSTLEVE, R.W.,
REMARK 3 JIANG, J.S., KUSZEWSKI, J., NILGES, M., PANNU,
REMARK 3 N.S., READ, R.J., RICE, L.M., SIMONSON, T., WARREN,
REMARK 3 G.L. (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE MODELS ARE BASED ON A TOTAL OF 1993 CONSTRAINTS (12.5
REMARK 3 CONSTRAINTS PER RESIDUE):
REMARK 3 1793 NOE-DERIVED DISTANCE CONSTRAINTS;
REMARK 3 116 TALOS-DERIVED DIHEDRAL ANGLE CONSTRAINTS;
REMARK 3 AND 84 HYDROGEN BOND CONSTRAINTS, BASED ON THE IDENTIFICATION OF
REMARK 3 SLOW EXCHANGE AMIDE PROTONS IN D2O NOESY AND TOCSY EXPERIMENTS,
REMARK 3 ON CHARACTERISTIC NOE PATTERNS FOR ALPHA-HELICES AND BETA-SHEETS,
REMARK 3 AND ON THE PROXIMITY AND ORIENTATION OF POTENTIAL HYDROGEN BOND
REMARK 3 PARTNERS IN ANNEALED STRUCTURES.
REMARK 3 THE FINAL SET OF 20 STRUCTURES CONTAINS NO VIOLATIONS OF NOE
REMARK 3 DISTANCE CONSTRAINTS GREATER THAN 0.15 ANGSTROMS
REMARK 3 AND NO VIOLATIONS OF DIHEDRAL ANGLE CONSTRAINTS GREATER THAN 5
REMARK 3 DEGREES.
REMARK 4
REMARK 4 1KRI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-02.
REMARK 100 THE DEPOSITION ID IS D_1000015266.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 20 MM NAPO4, 10 MM NACL, 0.02%
REMARK 210 NA AZIDE
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM ECVP8(46-231) U-15N; 1 MM
REMARK 210 ECVP8(46-231) U-15N, 13C, 2D;
REMARK 210 0.1 MM ECVP8(46-231) U-15N-ILE
REMARK 210 OR U-15N-LEU OR U-15N-PHE OR U-
REMARK 210 15N-TYR OR U-15N-VAL; 1 MM
REMARK 210 ECVP8(46-231) U-15N, 13C; 1 MM
REMARK 210 ECVP8(46-231) U-10% 13C; 1 MM
REMARK 210 ECVP8(46-231)
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC; HNCA; HN(CO)CA; HNCACB;
REMARK 210 HN(CO)CACB; HNCO; HN(CA)CO;
REMARK 210 HCCCONH; HNHA; HNHB; 3D-15N-
REMARK 210 SEPARATED TOCHSQC; HCCH-TOCSY;
REMARK 210 13C-HSQC; 2D-D2O-TOCSY; 3D-13C-
REMARK 210 SEPARATED NOESY; 3D-15N-
REMARK 210 SEPARATED NOEHSQC; 2D-D2O-NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; AVANCE; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5, TALOS,
REMARK 210 CNS 1.0
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 25
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
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: THE N-TERMINAL 19 RESIDUES (A46 TO V64 OF VP4)
REMARK 210 AND THE C-TERMINAL 7 RESIDUES (P225 TO R231 OF VP4) ARE DISORDERED
REMARK 210 AND ARE NOT INCLUDED IN THE MODELS.
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 ALA A 46
REMARK 465 PRO A 47
REMARK 465 VAL A 48
REMARK 465 ASN A 49
REMARK 465 TRP A 50
REMARK 465 GLY A 51
REMARK 465 PRO A 52
REMARK 465 GLY A 53
REMARK 465 GLU A 54
REMARK 465 THR A 55
REMARK 465 ASN A 56
REMARK 465 ASP A 57
REMARK 465 SER A 58
REMARK 465 THR A 59
REMARK 465 THR A 60
REMARK 465 VAL A 61
REMARK 465 GLU A 62
REMARK 465 PRO A 63
REMARK 465 VAL A 64
REMARK 465 PRO A 225
REMARK 465 PRO A 226
REMARK 465 ILE A 227
REMARK 465 GLN A 228
REMARK 465 ASN A 229
REMARK 465 THR A 230
REMARK 465 ARG A 231
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: 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 ASP A 66 -66.74 -98.43
REMARK 500 1 PRO A 68 80.26 -68.67
REMARK 500 1 PRO A 77 -160.86 -57.35
REMARK 500 1 ALA A 89 -175.17 -64.90
REMARK 500 1 THR A 99 -53.13 -139.99
REMARK 500 1 ASP A 100 42.56 -167.39
REMARK 500 1 ARG A 101 118.20 -175.64
REMARK 500 1 ASN A 111 95.18 56.08
REMARK 500 1 SER A 114 98.29 51.94
REMARK 500 1 SER A 151 -177.21 -68.17
REMARK 500 1 TYR A 152 85.36 -171.14
REMARK 500 1 LYS A 163 97.74 69.06
REMARK 500 1 LEU A 164 137.33 -175.60
REMARK 500 1 ASN A 183 54.61 -145.38
REMARK 500 1 THR A 192 -57.94 -136.98
REMARK 500 1 GLU A 212 42.49 -93.43
REMARK 500 1 ASN A 222 40.68 -150.33
REMARK 500 2 GLN A 70 175.98 -55.06
REMARK 500 2 THR A 72 157.24 177.20
REMARK 500 2 PRO A 77 174.37 -50.43
REMARK 500 2 THR A 99 -67.41 -143.50
REMARK 500 2 ASP A 100 39.98 -152.37
REMARK 500 2 ARG A 101 127.44 -170.32
REMARK 500 2 ASN A 111 85.35 54.48
REMARK 500 2 SER A 114 94.70 56.85
REMARK 500 2 ASN A 132 141.90 -172.68
REMARK 500 2 LYS A 163 79.72 61.74
REMARK 500 2 ASN A 171 -71.07 65.98
REMARK 500 2 CYS A 203 -158.94 -131.36
REMARK 500 2 GLU A 212 33.36 -96.13
REMARK 500 2 ASN A 222 61.43 -159.87
REMARK 500 3 PRO A 71 -81.71 -81.90
REMARK 500 3 THR A 72 -164.02 44.18
REMARK 500 3 PRO A 86 -169.55 -71.86
REMARK 500 3 THR A 87 25.22 -152.82
REMARK 500 3 ALA A 88 156.70 178.79
REMARK 500 3 THR A 99 -63.16 -152.17
REMARK 500 3 ASP A 100 42.45 -156.33
REMARK 500 3 ASN A 111 74.11 59.25
REMARK 500 3 LYS A 163 82.95 61.99
REMARK 500 3 ASN A 183 52.53 -142.49
REMARK 500 3 THR A 186 96.05 -69.55
REMARK 500 3 THR A 192 -56.63 -132.69
REMARK 500 3 GLU A 212 31.68 -95.56
REMARK 500 4 PRO A 68 81.27 -63.77
REMARK 500 4 THR A 72 -176.46 -170.08
REMARK 500 4 PRO A 77 -168.07 -75.70
REMARK 500 4 ALA A 85 67.90 -115.97
REMARK 500 4 THR A 99 -57.39 -143.99
REMARK 500 4 ASP A 100 49.24 -166.21
REMARK 500
REMARK 500 THIS ENTRY HAS 331 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1KQR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING
REMARK 900 DOMAIN IN COMPLEX WITH 2-O-METHYL-ALPHA-D-N-ACETYL NEURAMINIC ACID
REMARK 900 RELATED ID: 5275 RELATED DB: BMRB
DBREF 1KRI A 46 231 UNP P12473 VP4_ROTRH 46 231
SEQRES 1 A 186 ALA PRO VAL ASN TRP GLY PRO GLY GLU THR ASN ASP SER
SEQRES 2 A 186 THR THR VAL GLU PRO VAL LEU ASP GLY PRO TYR GLN PRO
SEQRES 3 A 186 THR THR PHE ASN PRO PRO VAL ASP TYR TRP MET LEU LEU
SEQRES 4 A 186 ALA PRO THR ALA ALA GLY VAL VAL VAL GLU GLY THR ASN
SEQRES 5 A 186 ASN THR ASP ARG TRP LEU ALA THR ILE LEU VAL GLU PRO
SEQRES 6 A 186 ASN VAL THR SER GLU THR ARG SER TYR THR LEU PHE GLY
SEQRES 7 A 186 THR GLN GLU GLN ILE THR ILE ALA ASN ALA SER GLN THR
SEQRES 8 A 186 GLN TRP LYS PHE ILE ASP VAL VAL LYS THR THR GLN ASN
SEQRES 9 A 186 GLY SER TYR SER GLN TYR GLY PRO LEU GLN SER THR PRO
SEQRES 10 A 186 LYS LEU TYR ALA VAL MET LYS HIS ASN GLY LYS ILE TYR
SEQRES 11 A 186 THR TYR ASN GLY GLU THR PRO ASN VAL THR THR LYS TYR
SEQRES 12 A 186 TYR SER THR THR ASN TYR ASP SER VAL ASN MET THR ALA
SEQRES 13 A 186 PHE CYS ASP PHE TYR ILE ILE PRO ARG GLU GLU GLU SER
SEQRES 14 A 186 THR CYS THR GLU TYR ILE ASN ASN GLY LEU PRO PRO ILE
SEQRES 15 A 186 GLN ASN THR ARG
HELIX 1 1 ASN A 193 VAL A 197 5 5
HELIX 2 2 GLU A 212 GLY A 223 1 12
SHEET 1 A 6 THR A 72 ASN A 75 0
SHEET 2 A 6 MET A 199 PHE A 202 -1 O ALA A 201 N THR A 72
SHEET 3 A 6 GLY A 90 ASN A 97 -1 N GLU A 94 O THR A 200
SHEET 4 A 6 ARG A 101 VAL A 108 -1 O LEU A 107 N GLY A 90
SHEET 5 A 6 TRP A 138 LYS A 145 -1 O LYS A 139 N VAL A 108
SHEET 6 A 6 SER A 153 SER A 160 -1 O LEU A 158 N PHE A 140
SHEET 1 B 5 ASP A 204 ILE A 208 0
SHEET 2 B 5 TYR A 80 ALA A 85 -1 N ALA A 85 O ASP A 204
SHEET 3 B 5 LEU A 164 HIS A 170 -1 O TYR A 165 N LEU A 84
SHEET 4 B 5 LYS A 173 THR A 181 -1 N TYR A 175 O MET A 168
SHEET 5 B 5 THR A 185 THR A 191 -1 N TYR A 189 O ILE A 174
SHEET 1 C 2 SER A 114 LEU A 121 0
SHEET 2 C 2 THR A 124 ALA A 131 -1 O ILE A 130 N GLU A 115
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 - b 5 2 Bytes