PDB Short entry for 2UZG HEADER HYDROLASE 27-APR-07 2UZG TITLE ZF-UBP DOMAIN OF VDU1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 33; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 36-130; COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 33, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 33, DEUBIQUITINATING ENZYME 33, VHL-INTERACTING COMPND 7 DEUBIQUITINATING ENZYME 1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; 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 UBL CONJUGATION PATHWAY, DE-UBIQUITINATION, ALTERNATIVE SPLICING, KEYWDS 2 METAL-BINDING, THIOL PROTEASE, UBL CONJUGATION, ZINC, VDU1, ZF-UBP, KEYWDS 3 PROTEASE, HYDROLASE, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.D.ALLEN,M.BYCROFT REVDAT 4 24-JAN-18 2UZG 1 SOURCE REVDAT 3 24-FEB-09 2UZG 1 VERSN REVDAT 2 11-SEP-07 2UZG 1 JRNL REVDAT 1 08-MAY-07 2UZG 0 JRNL AUTH M.D.ALLEN,M.BYCROFT JRNL TITL THE SOLUTION STRUCTURE OF THE ZNF UBP DOMAIN OF USP33/VDU1. JRNL REF PROTEIN SCI. V. 16 2072 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17766394 JRNL DOI 10.1110/PS.072967807 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 2UZG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032388. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG 3.3 REMARK 210 METHOD USED : CNS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED AND UNLABELLED PROTEIN 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 34 REMARK 465 SER A 35 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 CYS A 64 -168.24 -122.26 REMARK 500 1 GLN A 67 131.83 65.12 REMARK 500 1 PRO A 69 -167.44 -72.24 REMARK 500 1 ASN A 70 76.54 65.84 REMARK 500 1 GLN A 88 -72.32 -125.74 REMARK 500 1 VAL A 89 12.77 -141.58 REMARK 500 1 SER A 118 46.84 76.92 REMARK 500 1 LEU A 127 -78.22 -102.62 REMARK 500 2 ASN A 70 107.80 -44.62 REMARK 500 2 GLN A 88 -70.29 -121.67 REMARK 500 2 VAL A 89 18.80 -148.02 REMARK 500 2 SER A 118 49.01 77.61 REMARK 500 2 LYS A 126 115.03 -176.78 REMARK 500 2 LEU A 127 -79.10 63.43 REMARK 500 2 THR A 129 -40.76 -174.11 REMARK 500 3 ASN A 37 -77.35 -108.23 REMARK 500 3 HIS A 38 -51.85 -135.04 REMARK 500 3 PRO A 69 -157.03 -75.36 REMARK 500 3 ASN A 70 73.85 67.88 REMARK 500 3 GLN A 88 -73.25 -125.09 REMARK 500 3 VAL A 89 17.30 -145.34 REMARK 500 3 SER A 118 54.46 76.09 REMARK 500 3 LYS A 126 -178.33 61.56 REMARK 500 4 ASN A 37 -68.61 -94.34 REMARK 500 4 HIS A 38 -176.25 -59.96 REMARK 500 4 LYS A 65 78.40 -103.66 REMARK 500 4 PRO A 69 -159.68 -72.11 REMARK 500 4 ASN A 70 73.51 66.87 REMARK 500 4 GLN A 88 -72.00 -122.36 REMARK 500 4 VAL A 89 20.46 -147.87 REMARK 500 4 SER A 118 47.68 77.29 REMARK 500 4 LYS A 126 -45.17 -157.25 REMARK 500 4 LEU A 127 -66.74 69.68 REMARK 500 4 THR A 129 -45.86 -156.65 REMARK 500 5 ASN A 70 93.48 -45.72 REMARK 500 5 GLN A 88 -77.49 -126.89 REMARK 500 5 VAL A 89 16.58 -142.59 REMARK 500 5 SER A 118 51.19 77.03 REMARK 500 5 LYS A 119 -177.89 -170.81 REMARK 500 5 LYS A 126 32.28 -144.58 REMARK 500 6 CYS A 64 -169.98 -120.73 REMARK 500 6 PRO A 69 -156.45 -75.45 REMARK 500 6 ASN A 70 71.53 66.11 REMARK 500 6 GLN A 88 -78.13 -125.21 REMARK 500 6 TYR A 102 30.00 -91.56 REMARK 500 6 SER A 118 51.16 77.39 REMARK 500 6 LYS A 126 148.82 62.55 REMARK 500 7 CYS A 64 -169.17 -126.24 REMARK 500 7 LYS A 65 76.37 -118.95 REMARK 500 7 GLN A 67 149.94 61.72 REMARK 500 REMARK 500 THIS ENTRY HAS 153 RAMACHANDRAN OUTLIERS. 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 A 131 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 114 SG REMARK 620 2 CYS A 39 SG 98.6 REMARK 620 3 HIS A 41 ND1 100.1 94.7 REMARK 620 4 CYS A 117 SG 122.3 116.6 119.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 132 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 64 SG REMARK 620 2 HIS A 91 ND1 105.1 REMARK 620 3 CYS A 84 SG 114.9 107.3 REMARK 620 4 CYS A 61 SG 104.1 110.5 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 133 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 79 SG REMARK 620 2 HIS A 101 ND1 111.9 REMARK 620 3 CYS A 74 SG 114.4 94.6 REMARK 620 4 HIS A 95 NE2 112.1 110.3 112.4 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 A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 133 DBREF 2UZG A 34 35 PDB 2UZG 2UZG 34 35 DBREF 2UZG A 36 130 UNP Q8TEY7 UBP33_HUMAN 36 130 SEQRES 1 A 97 GLY SER ARG ASN HIS CYS PRO HIS LEU ASP SER VAL GLY SEQRES 2 A 97 GLU ILE THR LYS GLU ASP LEU ILE GLN LYS SER LEU GLY SEQRES 3 A 97 THR CYS GLN ASP CYS LYS VAL GLN GLY PRO ASN LEU TRP SEQRES 4 A 97 ALA CYS LEU GLU ASN ARG CYS SER TYR VAL GLY CYS GLY SEQRES 5 A 97 GLU SER GLN VAL ASP HIS SER THR ILE HIS SER GLN GLU SEQRES 6 A 97 THR LYS HIS TYR LEU THR VAL ASN LEU THR THR LEU ARG SEQRES 7 A 97 VAL TRP CYS TYR ALA CYS SER LYS GLU VAL PHE LEU ASP SEQRES 8 A 97 ARG LYS LEU GLY THR GLN HET ZN A 131 1 HET ZN A 132 1 HET ZN A 133 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 1 CYS A 39 VAL A 45 1 7 HELIX 2 2 THR A 49 SER A 57 1 9 HELIX 3 3 ASP A 90 THR A 99 1 10 SHEET 1 AA 5 VAL A 82 GLY A 83 0 SHEET 2 AA 5 TRP A 72 CYS A 74 -1 O TRP A 72 N GLY A 83 SHEET 3 AA 5 LEU A 103 ASN A 106 -1 O VAL A 105 N ALA A 73 SHEET 4 AA 5 ARG A 111 CYS A 114 -1 O ARG A 111 N ASN A 106 SHEET 5 AA 5 LYS A 119 VAL A 121 -1 O LYS A 119 N CYS A 114 LINK ZN ZN A 131 SG CYS A 114 1555 1555 2.32 LINK ZN ZN A 131 SG CYS A 39 1555 1555 2.35 LINK ZN ZN A 131 ND1 HIS A 41 1555 1555 2.04 LINK ZN ZN A 131 SG CYS A 117 1555 1555 2.23 LINK ZN ZN A 132 SG CYS A 64 1555 1555 2.35 LINK ZN ZN A 132 ND1 HIS A 91 1555 1555 2.09 LINK ZN ZN A 132 SG CYS A 84 1555 1555 2.35 LINK ZN ZN A 132 SG CYS A 61 1555 1555 2.35 LINK ZN ZN A 133 SG CYS A 79 1555 1555 2.35 LINK ZN ZN A 133 ND1 HIS A 101 1555 1555 2.05 LINK ZN ZN A 133 SG CYS A 74 1555 1555 2.35 LINK ZN ZN A 133 NE2 HIS A 95 1555 1555 2.05 CISPEP 1 GLY A 68 PRO A 69 1 -0.05 CISPEP 2 GLY A 68 PRO A 69 2 0.14 CISPEP 3 GLY A 68 PRO A 69 3 0.15 CISPEP 4 GLY A 68 PRO A 69 4 0.08 CISPEP 5 GLY A 68 PRO A 69 5 0.13 CISPEP 6 GLY A 68 PRO A 69 6 0.06 CISPEP 7 GLY A 68 PRO A 69 7 0.10 CISPEP 8 GLY A 68 PRO A 69 8 0.16 CISPEP 9 GLY A 68 PRO A 69 9 0.13 CISPEP 10 GLY A 68 PRO A 69 10 0.06 CISPEP 11 GLY A 68 PRO A 69 11 0.20 CISPEP 12 GLY A 68 PRO A 69 12 -0.06 CISPEP 13 GLY A 68 PRO A 69 13 0.27 CISPEP 14 GLY A 68 PRO A 69 14 0.09 CISPEP 15 GLY A 68 PRO A 69 15 0.04 CISPEP 16 GLY A 68 PRO A 69 16 0.11 CISPEP 17 GLY A 68 PRO A 69 17 0.10 CISPEP 18 GLY A 68 PRO A 69 18 0.16 CISPEP 19 GLY A 68 PRO A 69 19 0.08 CISPEP 20 GLY A 68 PRO A 69 20 0.13 SITE 1 AC1 4 CYS A 39 HIS A 41 CYS A 114 CYS A 117 SITE 1 AC2 4 CYS A 61 CYS A 64 CYS A 84 HIS A 91 SITE 1 AC3 5 CYS A 74 CYS A 79 HIS A 95 THR A 99 SITE 2 AC3 5 HIS A 101 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