PDB Short entry for 2L80 HEADER PROTEIN BINDING 28-DEC-10 2L80 TITLE SOLUTION STRUCTURE OF THE ZINC FINGER DOMAIN OF USP13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DOMAIN, UBP-TYPE, UNP RESIDUES 188-301; COMPND 5 SYNONYM: USP13, DEUBIQUITINATING ENZYME 13, ISOPEPTIDASE T-3, ISOT-3, COMPND 6 UBIQUITIN THIOLESTERASE 13, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE COMPND 7 13; 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: USP13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-M KEYWDS ZINC FINGER, USP13, UBIQUITIN BINDING, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.ZHANG,C.ZHOU,Z.ZHOU,A.SONG,H.HU REVDAT 2 14-JUN-23 2L80 1 REMARK SEQADV LINK REVDAT 1 14-DEC-11 2L80 0 JRNL AUTH Y.ZHANG,A.SONG,C.ZHOU,Z.ZHOU,H.HU JRNL TITL BIOCHEMICAL CHARACTERIZATION OF THE UBIQUITIN RECEPTORS IN JRNL TITL 2 USP13 REVEALS DIFFERENT CATALYTIC ACTIVATION OF JRNL TITL 3 DEUBIQUITINATION FROM ITS ANALOGUE USP5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000102071. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-15N] ENTITY; 20MM SODIUM REMARK 210 PHOSPHATE; 50MM SODIUM CHLORIDE; REMARK 210 90% H2O/10% D2O; 1MM [U-100% 13C; REMARK 210 U-100% 15N] ENTITY; 20MM SODIUM REMARK 210 PHOSPHATE; 50MM SODIUM CHLORIDE; REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNHA; 3D HNCO; 3D REMARK 210 C(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY 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 : NMRPIPE, TALOS, SPARKY, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 1-10 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: 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 OD2 ASP A 94 HD1 HIS A 100 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 TRP A 22 143.52 -178.78 REMARK 500 1 LYS A 23 139.10 177.10 REMARK 500 1 ALA A 25 -70.05 -63.92 REMARK 500 1 ARG A 26 -77.83 -58.70 REMARK 500 1 ASP A 28 52.78 -109.82 REMARK 500 1 THR A 38 -75.82 -91.37 REMARK 500 1 LEU A 43 -166.42 -122.84 REMARK 500 1 PHE A 48 -87.84 60.54 REMARK 500 1 PRO A 68 48.58 -91.57 REMARK 500 1 PRO A 95 5.04 -67.97 REMARK 500 1 HIS A 112 64.30 -164.56 REMARK 500 2 SER A 20 37.03 -79.02 REMARK 500 2 TRP A 22 175.92 62.85 REMARK 500 2 LYS A 23 143.91 177.91 REMARK 500 2 ARG A 26 -89.21 -88.42 REMARK 500 2 ASP A 28 38.49 -96.27 REMARK 500 2 THR A 38 -74.67 -93.82 REMARK 500 2 LYS A 46 -70.69 68.41 REMARK 500 2 ASP A 50 -81.29 -101.91 REMARK 500 2 SER A 51 -75.99 -128.84 REMARK 500 2 MET A 111 -74.34 -68.55 REMARK 500 2 HIS A 112 34.43 171.71 REMARK 500 3 TYR A 4 34.09 -92.31 REMARK 500 3 ASN A 7 46.23 -88.40 REMARK 500 3 ASN A 13 59.68 -141.69 REMARK 500 3 LYS A 23 141.60 -179.87 REMARK 500 3 ARG A 26 -90.56 -101.56 REMARK 500 3 ASP A 28 44.19 -90.83 REMARK 500 3 LYS A 46 88.53 -155.26 REMARK 500 3 TRP A 47 -79.09 -80.02 REMARK 500 3 SER A 52 -58.36 73.24 REMARK 500 3 TYR A 67 79.07 29.82 REMARK 500 3 PRO A 78 27.16 -72.68 REMARK 500 3 ASP A 79 -52.11 -140.99 REMARK 500 3 VAL A 92 -169.67 -118.70 REMARK 500 4 ASN A 7 67.08 -109.88 REMARK 500 4 ASN A 13 52.82 -96.70 REMARK 500 4 PRO A 19 -9.75 -57.14 REMARK 500 4 LYS A 23 134.55 176.73 REMARK 500 4 ARG A 26 -87.72 -89.33 REMARK 500 4 THR A 38 -82.71 -95.68 REMARK 500 4 PHE A 49 -29.97 -168.46 REMARK 500 4 ASP A 50 108.43 -57.70 REMARK 500 4 SER A 51 -58.71 -153.19 REMARK 500 4 TYR A 67 107.88 -59.04 REMARK 500 4 PRO A 68 42.54 -102.06 REMARK 500 4 PRO A 78 29.22 -71.21 REMARK 500 4 ASP A 79 -44.78 -132.25 REMARK 500 4 VAL A 92 -164.87 -119.35 REMARK 500 4 PRO A 95 1.40 -68.63 REMARK 500 REMARK 500 THIS ENTRY HAS 111 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 124 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 109.9 REMARK 620 3 CYS A 44 SG 109.5 111.3 REMARK 620 4 HIS A 57 NE2 109.7 109.7 106.7 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 124 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17388 RELATED DB: BMRB DBREF 2L80 A 1 114 UNP Q92995 UBP13_HUMAN 188 301 SEQADV 2L80 GLY A -1 UNP Q92995 EXPRESSION TAG SEQADV 2L80 SER A 0 UNP Q92995 EXPRESSION TAG SEQRES 1 A 116 GLY SER VAL SER LYS TYR ALA ASN ASN LEU THR GLN LEU SEQRES 2 A 116 ASP ASN GLY VAL ARG ILE PRO PRO SER GLY TRP LYS CYS SEQRES 3 A 116 ALA ARG CYS ASP LEU ARG GLU ASN LEU TRP LEU ASN LEU SEQRES 4 A 116 THR ASP GLY SER VAL LEU CYS GLY LYS TRP PHE PHE ASP SEQRES 5 A 116 SER SER GLY GLY ASN GLY HIS ALA LEU GLU HIS TYR ARG SEQRES 6 A 116 ASP MET GLY TYR PRO LEU ALA VAL LYS LEU GLY THR ILE SEQRES 7 A 116 THR PRO ASP GLY ALA ASP VAL TYR SER PHE GLN GLU GLU SEQRES 8 A 116 GLU PRO VAL LEU ASP PRO HIS LEU ALA LYS HIS LEU ALA SEQRES 9 A 116 HIS PHE GLY ILE ASP MET LEU HIS MET HIS GLY THR HET ZN A 124 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 GLY A 56 MET A 65 1 10 HELIX 2 2 HIS A 96 PHE A 104 1 9 HELIX 3 3 MET A 108 GLY A 113 1 6 SHEET 1 A 5 VAL A 42 CYS A 44 0 SHEET 2 A 5 LEU A 33 ASN A 36 -1 N TRP A 34 O LEU A 43 SHEET 3 A 5 LEU A 69 LEU A 73 -1 O VAL A 71 N LEU A 35 SHEET 4 A 5 ASP A 82 SER A 85 -1 O TYR A 84 N ALA A 70 SHEET 5 A 5 PRO A 91 VAL A 92 -1 O VAL A 92 N VAL A 83 LINK SG CYS A 24 ZN ZN A 124 1555 1555 2.29 LINK SG CYS A 27 ZN ZN A 124 1555 1555 2.30 LINK SG CYS A 44 ZN ZN A 124 1555 1555 2.28 LINK NE2 HIS A 57 ZN ZN A 124 1555 1555 1.99 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 44 HIS A 57 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