HEADER ZINC-BINDING PROTEIN 07-MAY-04 1VYX TITLE SOLUTION STRUCTURE OF THE KSHV K3 N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF K3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING FINGER, RESIDUES 1-60; COMPND 5 SYNONYM: K3RING; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 8; SOURCE 3 ORGANISM_COMMON: KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS; SOURCE 4 ORGANISM_TAXID: 37296; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA KEYWDS ZINC-BINDING PROTEIN, RING DOMAIN, CROSS-BRACE MOTIF EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR R.B.DODD,M.D.ALLEN,S.E.BROWN,C.M.SANDERSON,L.M.DUNCAN,P.J.LEHNER, AUTHOR 2 M.BYCROFT,R.J.READ REVDAT 7 02-MAY-18 1VYX 1 REMARK REVDAT 6 24-JAN-18 1VYX 1 SOURCE REVDAT 5 24-FEB-09 1VYX 1 VERSN REVDAT 4 03-MAY-05 1VYX 1 ATOM REVDAT 3 19-JAN-05 1VYX 1 REVDAT REVDAT 2 15-DEC-04 1VYX 1 JRNL REVDAT 1 01-OCT-04 1VYX 0 JRNL AUTH R.B.DODD,M.D.ALLEN,S.E.BROWN,C.M.SANDERSON,L.M.DUNCAN, JRNL AUTH 2 P.J.LEHNER,M.BYCROFT,R.J.READ JRNL TITL SOLUTION STRUCTURE OF THE KAPOSI'S SARCOMA-ASSOCIATED JRNL TITL 2 HERPESVIRUS K3 N-TERMINAL DOMAIN REVEALS A NOVEL E2-BINDING JRNL TITL 3 C4HC3-TYPE RING DOMAIN JRNL REF J.BIOL.CHEM. V. 279 53840 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15465811 JRNL DOI 10.1074/JBC.M409662200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1VYX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290020025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100.0 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 50 MM POTASSIUM PHOSPHATE (PH REMARK 210 6.0), CONTAINING 50 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; HNCACB; REMARK 210 CBCACONH; HNCO; HNCACO; 13C-HSQC; REMARK 210 HNHB REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWIN-NMR, ANSIG, XPLOR3.8 REMARK 210 METHOD USED : XPLOR3.8 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS GREATER THAN REMARK 210 0.25A, NO ANGLE VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDAR TRIPLE- REMARK 210 RESONANCE METHODS ON 13C-15N-LABELLED K3-RING DOMAIN 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 H CYS A 50 O VAL A 55 1.57 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 GLU A 4 -175.90 -49.68 REMARK 500 1 ASP A 5 153.54 70.28 REMARK 500 1 ASN A 18 39.21 169.99 REMARK 500 1 GLU A 19 106.45 -59.31 REMARK 500 1 ARG A 20 96.15 -62.26 REMARK 500 1 CYS A 24 166.70 172.77 REMARK 500 1 CYS A 26 -161.68 -76.19 REMARK 500 1 ARG A 46 64.19 68.94 REMARK 500 1 ASN A 58 72.63 49.47 REMARK 500 2 GLU A 2 -145.18 35.25 REMARK 500 2 ASP A 3 -74.42 -95.29 REMARK 500 2 ASN A 18 73.49 145.82 REMARK 500 2 ARG A 20 96.49 -61.56 REMARK 500 2 CYS A 26 -158.99 36.79 REMARK 500 3 ASP A 3 -163.52 -100.56 REMARK 500 3 ASP A 5 -175.13 52.45 REMARK 500 3 ASN A 18 55.16 119.12 REMARK 500 3 ARG A 20 98.47 -61.62 REMARK 500 3 ALA A 23 -32.16 -139.13 REMARK 500 3 CYS A 26 -101.76 -62.59 REMARK 500 3 ARG A 46 75.91 57.10 REMARK 500 3 ASN A 58 82.13 40.59 REMARK 500 4 ASP A 3 -151.03 -142.25 REMARK 500 4 GLU A 4 -101.94 -115.37 REMARK 500 4 ASP A 5 160.96 60.57 REMARK 500 4 ASN A 18 39.89 167.78 REMARK 500 4 GLU A 19 106.48 -59.07 REMARK 500 4 ARG A 20 95.76 -62.55 REMARK 500 4 CYS A 24 166.74 173.05 REMARK 500 4 CYS A 26 -162.12 -79.60 REMARK 500 4 ARG A 46 68.21 69.64 REMARK 500 4 ASN A 58 92.24 43.94 REMARK 500 5 GLU A 4 -40.60 -157.35 REMARK 500 5 ASP A 5 81.63 -69.31 REMARK 500 5 ASN A 13 60.97 64.23 REMARK 500 5 ASN A 18 32.69 -168.71 REMARK 500 5 ARG A 20 95.20 -66.61 REMARK 500 5 CYS A 24 167.86 171.79 REMARK 500 5 CYS A 26 -158.06 40.06 REMARK 500 5 ARG A 46 63.25 61.59 REMARK 500 6 GLU A 2 -76.77 -145.21 REMARK 500 6 ASP A 5 111.53 56.19 REMARK 500 6 ASN A 18 44.65 167.00 REMARK 500 6 GLU A 19 105.37 -59.10 REMARK 500 6 ARG A 20 95.56 -62.09 REMARK 500 6 CYS A 24 166.68 176.42 REMARK 500 6 CYS A 26 -168.49 -76.20 REMARK 500 6 ARG A 46 73.86 39.79 REMARK 500 6 THR A 48 -26.15 74.38 REMARK 500 7 ASP A 3 -168.33 49.44 REMARK 500 REMARK 500 THIS ENTRY HAS 237 RAMACHANDRAN OUTLIERS. 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 20 0.31 SIDE CHAIN REMARK 500 1 ARG A 22 0.22 SIDE CHAIN REMARK 500 1 ARG A 35 0.29 SIDE CHAIN REMARK 500 1 ARG A 46 0.32 SIDE CHAIN REMARK 500 1 ARG A 60 0.29 SIDE CHAIN REMARK 500 2 ARG A 20 0.24 SIDE CHAIN REMARK 500 2 ARG A 22 0.28 SIDE CHAIN REMARK 500 2 ARG A 35 0.30 SIDE CHAIN REMARK 500 2 ARG A 46 0.10 SIDE CHAIN REMARK 500 2 ARG A 60 0.28 SIDE CHAIN REMARK 500 3 ARG A 20 0.32 SIDE CHAIN REMARK 500 3 ARG A 22 0.28 SIDE CHAIN REMARK 500 3 ARG A 35 0.14 SIDE CHAIN REMARK 500 3 ARG A 46 0.32 SIDE CHAIN REMARK 500 3 ARG A 60 0.10 SIDE CHAIN REMARK 500 4 ARG A 20 0.31 SIDE CHAIN REMARK 500 4 ARG A 22 0.26 SIDE CHAIN REMARK 500 4 ARG A 35 0.27 SIDE CHAIN REMARK 500 4 ARG A 46 0.32 SIDE CHAIN REMARK 500 4 ARG A 60 0.26 SIDE CHAIN REMARK 500 5 ARG A 20 0.24 SIDE CHAIN REMARK 500 5 ARG A 22 0.29 SIDE CHAIN REMARK 500 5 ARG A 35 0.22 SIDE CHAIN REMARK 500 5 ARG A 46 0.19 SIDE CHAIN REMARK 500 6 ARG A 20 0.27 SIDE CHAIN REMARK 500 6 ARG A 22 0.20 SIDE CHAIN REMARK 500 6 ARG A 35 0.25 SIDE CHAIN REMARK 500 6 ARG A 46 0.27 SIDE CHAIN REMARK 500 6 ARG A 60 0.28 SIDE CHAIN REMARK 500 7 ARG A 20 0.27 SIDE CHAIN REMARK 500 7 ARG A 22 0.20 SIDE CHAIN REMARK 500 7 ARG A 35 0.22 SIDE CHAIN REMARK 500 7 ARG A 46 0.31 SIDE CHAIN REMARK 500 7 ARG A 60 0.26 SIDE CHAIN REMARK 500 8 ARG A 20 0.23 SIDE CHAIN REMARK 500 8 ARG A 22 0.26 SIDE CHAIN REMARK 500 8 ARG A 35 0.13 SIDE CHAIN REMARK 500 8 ARG A 46 0.20 SIDE CHAIN REMARK 500 8 ARG A 60 0.31 SIDE CHAIN REMARK 500 9 ARG A 20 0.15 SIDE CHAIN REMARK 500 9 ARG A 22 0.22 SIDE CHAIN REMARK 500 9 ARG A 35 0.29 SIDE CHAIN REMARK 500 9 ARG A 46 0.32 SIDE CHAIN REMARK 500 9 ARG A 60 0.32 SIDE CHAIN REMARK 500 10 ARG A 20 0.30 SIDE CHAIN REMARK 500 10 ARG A 22 0.30 SIDE CHAIN REMARK 500 10 ARG A 35 0.08 SIDE CHAIN REMARK 500 10 ARG A 46 0.31 SIDE CHAIN REMARK 500 10 ARG A 60 0.30 SIDE CHAIN REMARK 500 11 ARG A 20 0.30 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 136 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1061 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 37 SG REMARK 620 2 CYS A 12 SG 119.1 REMARK 620 3 CYS A 9 SG 95.2 102.1 REMARK 620 4 HIS A 34 ND1 132.9 100.6 100.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1062 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 50 SG 106.6 REMARK 620 3 CYS A 26 SG 104.6 122.3 REMARK 620 4 CYS A 53 SG 100.9 106.1 114.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1061 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1062 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CHC RELATED DB: PDB REMARK 900 EQUINE HERPES VIRUS-1 (C3HC4, OR RING DOMAIN) (NMR, 1 STRUCTURE) DBREF 1VYX A 1 60 UNP P90495 P90495 1 60 SEQRES 1 A 60 MET GLU ASP GLU ASP VAL PRO VAL CYS TRP ILE CYS ASN SEQRES 2 A 60 GLU GLU LEU GLY ASN GLU ARG PHE ARG ALA CYS GLY CYS SEQRES 3 A 60 THR GLY GLU LEU GLU ASN VAL HIS ARG SER CYS LEU SER SEQRES 4 A 60 THR TRP LEU THR ILE SER ARG ASN THR ALA CYS GLN ILE SEQRES 5 A 60 CYS GLY VAL VAL TYR ASN THR ARG HET ZN A1061 1 HET ZN A1062 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLY A 28 ASN A 32 5 5 HELIX 2 2 HIS A 34 ARG A 46 1 13 SHEET 1 AA 2 VAL A 8 CYS A 9 0 SHEET 2 AA 2 GLU A 14 GLU A 15 -1 O GLU A 14 N CYS A 9 LINK ZN ZN A1061 SG CYS A 37 1555 1555 2.28 LINK ZN ZN A1061 SG CYS A 12 1555 1555 2.33 LINK ZN ZN A1061 SG CYS A 9 1555 1555 2.41 LINK ZN ZN A1061 ND1 HIS A 34 1555 1555 2.20 LINK ZN ZN A1062 SG CYS A 24 1555 1555 2.20 LINK ZN ZN A1062 SG CYS A 50 1555 1555 2.28 LINK ZN ZN A1062 SG CYS A 26 1555 1555 2.27 LINK ZN ZN A1062 SG CYS A 53 1555 1555 2.35 SITE 1 AC1 4 CYS A 9 CYS A 12 HIS A 34 CYS A 37 SITE 1 AC2 4 CYS A 24 CYS A 26 CYS A 50 CYS A 53 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