PDB Short entry for 2KVR HEADER PROTEIN BINDING 25-MAR-10 2KVR TITLE SOLUTION NMR STRUCTURE OF HUMAN UBIQUITIN SPECIFIC PROTEASE USP7 UBL TITLE 2 DOMAIN (RESIDUES 537-664). NESG TARGET HR4395C/ SGC-TORONTO COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN (RESIDUES 537-664); COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 7, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 7, DEUBIQUITINATING ENZYME 7, HERPESVIRUS-ASSOCIATED COMPND 7 UBIQUITIN-SPECIFIC PROTEASE; COMPND 8 EC: 3.1.2.15; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS USP7, UBIQUITIN-LIKE DOMAIN, UBL, UBIQUITIN SPECIFIC PROTEASE, HOST- KEYWDS 2 VIRUS INTERACTION, HYDROLASE, NUCLEUS, PROTEASE, THIOL PROTEASE, KEYWDS 3 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 4 STRUCTURAL GENOMICS CONSORTIUM, NESG, SGC, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.BEZSONOVA,A.LEMAK,G.AVVAKUMOV,S.XUE,S.DHE-PAGANON,G.T.MONTELIONE, AUTHOR 2 C.ARROWSMITH,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 14-JUN-23 2KVR 1 REMARK REVDAT 3 05-FEB-20 2KVR 1 REMARK REVDAT 2 23-MAY-12 2KVR 1 REMARK VERSN REVDAT 1 21-APR-10 2KVR 0 JRNL AUTH I.BEZSONOVA,A.LEMAK,G.AVVAKUMOV,S.XUE,S.DHE-PAGANON, JRNL AUTH 2 G.T.MONTELIONE,C.ARROWSMITH JRNL TITL SOLUTION STRUCTURE OF THE UBIQUITIN SPECIFIC PROTEASE USP7 JRNL TITL 2 UBIQUITIN-LIKE DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LEMAK,A.GUTMANAS,S.CHITAYAT,M.KARRA,C.FARES,M.SUNNERHAGEN, REMARK 1 AUTH 2 C.H.ARROWSMITH REMARK 1 TITL A NOVEL STRATEGY FOR NMR RESONANCE ASSIGNMENT AND PROTEIN REMARK 1 TITL 2 STRUCTURE DETERMINATION. REMARK 1 REF J.BIOMOL.NMR V. 49 27 2011 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 21161328 REMARK 1 DOI 10.1007/S10858-010-9458-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, CYANA 2.1 REMARK 3 AUTHORS : FRANK DELAGLIO (NMRPIPE), PETER GUNTERT (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000101633. 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 : 250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8-1.2 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 20 MM SODIUM REMARK 210 PHOSPHATE, PH 7.0, 250 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 0.5 MM PMSF, REMARK 210 1 MM BENZAMIDINE, 1 MM TCEP, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HBHA(CO)NH; REMARK 210 3D CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D AROMATIC 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ABACUS, CYANA 2.1, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 GLY A -1 REMARK 465 SER A 0 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 LYS A 20 99.28 -42.29 REMARK 500 1 ALA A 25 -151.39 -155.02 REMARK 500 1 TYR A 28 29.89 -58.56 REMARK 500 1 MET A 29 125.84 -31.93 REMARK 500 1 CYS A 40 -75.62 -157.27 REMARK 500 1 MET A 47 -157.20 -78.22 REMARK 500 1 LYS A 52 40.22 -104.03 REMARK 500 1 TYR A 55 99.90 -50.68 REMARK 500 1 ASP A 107 33.21 -90.78 REMARK 500 2 LYS A 20 91.57 -66.72 REMARK 500 2 GLU A 21 88.41 57.37 REMARK 500 2 TYR A 28 27.10 -62.37 REMARK 500 2 MET A 29 121.43 -29.68 REMARK 500 2 HIS A 42 38.00 75.30 REMARK 500 2 MET A 47 63.62 -110.46 REMARK 500 2 TYR A 55 108.36 -49.41 REMARK 500 2 ILE A 84 93.31 -69.42 REMARK 500 2 MET A 89 89.83 -66.21 REMARK 500 2 ALA A 91 85.15 -69.08 REMARK 500 2 ASP A 103 98.96 -63.30 REMARK 500 2 ASP A 107 38.64 -84.27 REMARK 500 2 ASN A 118 31.45 73.41 REMARK 500 3 GLN A 23 -45.20 -178.51 REMARK 500 3 TYR A 28 28.79 -68.66 REMARK 500 3 MET A 29 134.04 -35.95 REMARK 500 3 GLU A 36 118.22 -162.56 REMARK 500 3 HIS A 42 -50.02 -122.54 REMARK 500 3 ASP A 46 18.72 -156.94 REMARK 500 3 LYS A 54 -176.70 -69.83 REMARK 500 3 TYR A 55 106.59 -49.91 REMARK 500 3 SER A 93 47.65 -85.03 REMARK 500 3 ASP A 103 88.35 -69.72 REMARK 500 3 ASP A 107 36.90 -88.21 REMARK 500 3 ASN A 118 -7.69 77.21 REMARK 500 4 ARG A 22 -51.90 -174.28 REMARK 500 4 TYR A 28 26.84 -62.67 REMARK 500 4 MET A 29 124.52 -33.74 REMARK 500 4 HIS A 42 -70.07 68.20 REMARK 500 4 LYS A 54 178.35 -51.96 REMARK 500 4 TYR A 55 103.77 -48.12 REMARK 500 4 MET A 89 92.57 -61.15 REMARK 500 4 ARG A 98 66.47 -152.37 REMARK 500 5 ALA A 25 -149.67 -135.54 REMARK 500 5 HIS A 26 8.51 -69.56 REMARK 500 5 TYR A 28 27.15 -65.95 REMARK 500 5 MET A 29 139.53 -39.80 REMARK 500 5 ASN A 45 -159.90 -77.26 REMARK 500 5 ASP A 46 -33.41 -134.95 REMARK 500 5 LYS A 54 -164.17 -74.99 REMARK 500 5 TYR A 55 102.56 -53.22 REMARK 500 REMARK 500 THIS ENTRY HAS 226 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16789 RELATED DB: BMRB REMARK 900 RELATED ID: HR4395 RELATED DB: TARGETDB DBREF 2KVR A 1 128 UNP Q93009 UBP7_HUMAN 537 664 SEQADV 2KVR GLY A -1 UNP Q93009 EXPRESSION TAG SEQADV 2KVR SER A 0 UNP Q93009 EXPRESSION TAG SEQRES 1 A 130 GLY SER PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU GLU SEQRES 2 A 130 LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU ARG GLN GLU SEQRES 3 A 130 ALA HIS LEU TYR MET GLN VAL GLN ILE VAL ALA GLU ASP SEQRES 4 A 130 GLN PHE CYS GLY HIS GLN GLY ASN ASP MET TYR ASP GLU SEQRES 5 A 130 GLU LYS VAL LYS TYR THR VAL PHE LYS VAL LEU LYS ASN SEQRES 6 A 130 SER SER LEU ALA GLU PHE VAL GLN SER LEU SER GLN THR SEQRES 7 A 130 MET GLY PHE PRO GLN ASP GLN ILE ARG LEU TRP PRO MET SEQRES 8 A 130 GLN ALA ARG SER ASN GLY THR LYS ARG PRO ALA MET LEU SEQRES 9 A 130 ASP ASN GLU ALA ASP GLY ASN LYS THR MET ILE GLU LEU SEQRES 10 A 130 SER ASP ASN GLU ASN PRO TRP THR ILE PHE LEU GLU THR HELIX 1 1 GLN A 2 ARG A 13 1 12 HELIX 2 2 ILE A 14 ARG A 19 1 6 HELIX 3 3 SER A 65 GLY A 78 1 14 HELIX 4 4 PRO A 80 ILE A 84 5 5 HELIX 5 5 GLU A 105 ASN A 109 5 5 HELIX 6 6 MET A 112 ASP A 117 1 6 SHEET 1 A 4 THR A 56 LYS A 59 0 SHEET 2 A 4 GLN A 30 VAL A 34 -1 N ILE A 33 O THR A 56 SHEET 3 A 4 TRP A 122 GLU A 127 1 O ILE A 124 N GLN A 32 SHEET 4 A 4 ARG A 85 PRO A 88 -1 N TRP A 87 O PHE A 125 CISPEP 1 ASN A 120 PRO A 121 1 -0.02 CISPEP 2 ASN A 120 PRO A 121 2 -0.71 CISPEP 3 ASN A 120 PRO A 121 3 1.34 CISPEP 4 ASN A 120 PRO A 121 4 -2.14 CISPEP 5 ASN A 120 PRO A 121 5 -4.05 CISPEP 6 ASN A 120 PRO A 121 6 -3.39 CISPEP 7 ASN A 120 PRO A 121 7 -1.43 CISPEP 8 ASN A 120 PRO A 121 8 -3.41 CISPEP 9 ASN A 120 PRO A 121 9 -0.84 CISPEP 10 ASN A 120 PRO A 121 10 -4.90 CISPEP 11 ASN A 120 PRO A 121 11 -1.08 CISPEP 12 ASN A 120 PRO A 121 12 -6.70 CISPEP 13 ASN A 120 PRO A 121 13 3.51 CISPEP 14 ASN A 120 PRO A 121 14 -2.50 CISPEP 15 ASN A 120 PRO A 121 15 3.56 CISPEP 16 ASN A 120 PRO A 121 16 0.25 CISPEP 17 ASN A 120 PRO A 121 17 6.41 CISPEP 18 ASN A 120 PRO A 121 18 -5.52 CISPEP 19 ASN A 120 PRO A 121 19 -4.39 CISPEP 20 ASN A 120 PRO A 121 20 0.24 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