PDB Short entry for 6KCZ HEADER HYDROLASE 30-JUN-19 6KCZ TITLE SOLUTION STRUCTURE OF THE ZNF-UBP DOMAIN OF USP20/VDU2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 20; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 20,UBIQUITIN THIOESTERASE 20, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 20,VHL-INTERACTING COMPND 6 DEUBIQUITINATING ENZYME 2,HVDU2; COMPND 7 EC: 3.4.19.12; 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 GENE: USP20, KIAA1003, LSFR3A, VDU2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.YANG,Y.WEN,N.ZHANG REVDAT 4 14-JUN-23 6KCZ 1 REMARK REVDAT 3 04-SEP-19 6KCZ 1 JRNL REVDAT 2 21-AUG-19 6KCZ 1 SPRSDE JRNL REVDAT 1 17-JUL-19 6KCZ 0 SPRSDE 21-AUG-19 6KCZ 5Z4I JRNL AUTH Y.YANG,Y.DING,C.ZHOU,Y.WEN,N.ZHANG JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF USP20 ZNF-UBP DOMAIN BY JRNL TITL 2 NMR. JRNL REF PROTEIN SCI. V. 28 1606 2019 JRNL REFN ESSN 1469-896X JRNL PMID 31278784 JRNL DOI 10.1002/PRO.3675 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012723. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-99% 13C; U-99% 15N] REMARK 210 USP20, 90% H2O/10% D2O; 0.6 MM REMARK 210 [U-99% 15N] USP20, 90% H2O/10% REMARK 210 D2O; 0.6 MM [U-99% 13C] USP20, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D 1H- REMARK 210 15N NOESY; 2D 1H-13C HSQC; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D HCCH- REMARK 210 TOCSY; 3D H(CCO)NH; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 O LEU A 24 H LYS A 27 1.49 REMARK 500 H ASN A 39 OG1 THR A 77 1.55 REMARK 500 N ASN A 39 OG1 THR A 77 2.12 REMARK 500 O GLY A 54 N SER A 56 2.15 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 SER A 4 168.16 55.41 REMARK 500 1 SER A 26 11.21 -68.33 REMARK 500 1 THR A 36 -177.01 166.30 REMARK 500 1 VAL A 46 -20.09 -39.57 REMARK 500 1 ALA A 47 54.45 -149.29 REMARK 500 1 GLU A 55 -37.46 -25.62 REMARK 500 1 SER A 56 -43.47 -28.33 REMARK 500 1 PHE A 57 -92.08 -118.44 REMARK 500 1 LYS A 69 16.54 56.01 REMARK 500 1 LEU A 76 9.01 -68.29 REMARK 500 1 PHE A 79 56.53 79.48 REMARK 500 1 TYR A 84 2.61 -68.77 REMARK 500 1 ALA A 85 -71.35 -99.87 REMARK 500 1 GLU A 93 2.04 -46.73 REMARK 500 1 GLN A 94 -19.89 61.36 REMARK 500 1 ALA A 97 146.38 -171.58 REMARK 500 2 SER A 4 -172.80 168.24 REMARK 500 2 THR A 36 -176.94 166.64 REMARK 500 2 VAL A 46 -20.95 -39.45 REMARK 500 2 ALA A 47 52.96 -150.13 REMARK 500 2 GLU A 55 -37.34 -25.78 REMARK 500 2 SER A 56 -43.39 -28.47 REMARK 500 2 PHE A 57 -92.28 -118.24 REMARK 500 2 LYS A 69 16.71 56.87 REMARK 500 2 LEU A 76 7.02 -67.87 REMARK 500 2 PHE A 79 54.62 78.99 REMARK 500 2 TYR A 84 2.49 -69.86 REMARK 500 2 ALA A 85 -70.77 -100.67 REMARK 500 2 GLU A 93 2.44 -49.79 REMARK 500 2 GLN A 94 -20.08 63.86 REMARK 500 2 ALA A 97 87.32 -154.47 REMARK 500 2 ALA A 98 71.71 -163.26 REMARK 500 3 ASP A 3 102.65 54.90 REMARK 500 3 SER A 4 -176.82 168.30 REMARK 500 3 SER A 26 11.64 -69.58 REMARK 500 3 THR A 36 -176.58 165.13 REMARK 500 3 TRP A 41 93.56 -161.75 REMARK 500 3 VAL A 46 -20.54 -39.63 REMARK 500 3 ALA A 47 47.31 -147.66 REMARK 500 3 GLU A 55 -37.21 -24.51 REMARK 500 3 SER A 56 -42.80 -29.03 REMARK 500 3 PHE A 57 -92.91 -117.79 REMARK 500 3 LYS A 69 16.50 47.75 REMARK 500 3 PHE A 79 49.87 79.59 REMARK 500 3 TYR A 84 2.54 -68.09 REMARK 500 3 ALA A 85 -70.26 -100.60 REMARK 500 3 GLU A 93 2.33 -49.57 REMARK 500 3 GLN A 94 -19.74 61.00 REMARK 500 3 ALA A 98 59.22 -156.77 REMARK 500 4 ASP A 3 -124.31 -84.85 REMARK 500 REMARK 500 THIS ENTRY HAS 361 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 HIS A 10 ND1 114.0 REMARK 620 3 CYS A 83 SG 108.7 103.4 REMARK 620 4 CYS A 86 SG 113.6 102.3 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 107.9 REMARK 620 3 CYS A 53 SG 116.3 107.4 REMARK 620 4 HIS A 60 ND1 115.0 102.2 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 43 SG REMARK 620 2 CYS A 48 SG 107.5 REMARK 620 3 HIS A 64 NE2 107.7 109.9 REMARK 620 4 HIS A 70 ND1 111.9 106.3 113.3 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26901 RELATED DB: BMRB DBREF 6KCZ A 1 99 UNP Q9Y2K6 UBP20_HUMAN 1 99 SEQRES 1 A 99 MET GLY ASP SER ARG ASP LEU CYS PRO HIS LEU ASP SER SEQRES 2 A 99 ILE GLY GLU VAL THR LYS GLU ASP LEU LEU LEU LYS SER SEQRES 3 A 99 LYS GLY THR CYS GLN SER CYS GLY VAL THR GLY PRO ASN SEQRES 4 A 99 LEU TRP ALA CYS LEU GLN VAL ALA CYS PRO TYR VAL GLY SEQRES 5 A 99 CYS GLY GLU SER PHE ALA ASP HIS SER THR ILE HIS ALA SEQRES 6 A 99 GLN ALA LYS LYS HIS ASN LEU THR VAL ASN LEU THR THR SEQRES 7 A 99 PHE ARG LEU TRP CYS TYR ALA CYS GLU LYS GLU VAL PHE SEQRES 8 A 99 LEU GLU GLN ARG LEU ALA ALA PRO HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 AA1 THR A 18 SER A 26 1 9 HELIX 2 AA2 ASP A 59 LYS A 68 1 10 SHEET 1 AA1 5 VAL A 51 GLY A 52 0 SHEET 2 AA1 5 TRP A 41 CYS A 43 -1 N TRP A 41 O GLY A 52 SHEET 3 AA1 5 LEU A 72 VAL A 74 -1 O VAL A 74 N ALA A 42 SHEET 4 AA1 5 LEU A 81 CYS A 83 -1 O TRP A 82 N THR A 73 SHEET 5 AA1 5 LYS A 88 VAL A 90 -1 O VAL A 90 N LEU A 81 LINK SG CYS A 8 ZN ZN A 101 1555 1555 2.32 LINK ND1 HIS A 10 ZN ZN A 101 1555 1555 2.02 LINK SG CYS A 30 ZN ZN A 102 1555 1555 2.32 LINK SG CYS A 33 ZN ZN A 102 1555 1555 2.30 LINK SG CYS A 43 ZN ZN A 103 1555 1555 2.29 LINK SG CYS A 48 ZN ZN A 103 1555 1555 2.29 LINK SG CYS A 53 ZN ZN A 102 1555 1555 2.30 LINK ND1 HIS A 60 ZN ZN A 102 1555 1555 2.01 LINK NE2 HIS A 64 ZN ZN A 103 1555 1555 1.99 LINK ND1 HIS A 70 ZN ZN A 103 1555 1555 1.99 LINK SG CYS A 83 ZN ZN A 101 1555 1555 2.29 LINK SG CYS A 86 ZN ZN A 101 1555 1555 2.32 SITE 1 AC1 5 CYS A 8 PRO A 9 HIS A 10 CYS A 83 SITE 2 AC1 5 CYS A 86 SITE 1 AC2 4 CYS A 30 CYS A 33 CYS A 53 HIS A 60 SITE 1 AC3 4 CYS A 43 CYS A 48 HIS A 64 HIS A 70 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