HEADER HYDROLASE 23-AUG-06 2I50 TITLE SOLUTION STRUCTURE OF UBP-M ZNF-UBP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 16; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZNF-UBP DOMAIN, RESIDUES 22-143; COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 16, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 16, DEUBIQUITINATING ENZYME 16, UBIQUITIN-PROCESSING COMPND 7 PROTEASE UBP-M; 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: USP16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ALPHA/BETA ZINC-FINGER, RING-FINGER, ZNF-UBP, METALLOPROTEIN, KEYWDS 2 UBIQUITIN-BINDING PROTEIN, USP, UBIQUITIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.-T.PAI REVDAT 3 09-MAR-22 2I50 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2I50 1 VERSN REVDAT 1 07-AUG-07 2I50 0 JRNL AUTH M.T.PAI,S.R.TZENG,J.J.KOVACS,M.A.KEATON,S.S.LI,T.P.YAO, JRNL AUTH 2 P.ZHOU JRNL TITL SOLUTION STRUCTURE OF THE UBP-M BUZ DOMAIN, A HIGHLY JRNL TITL 2 SPECIFIC PROTEIN MODULE THAT RECOGNIZES THE C-TERMINAL TAIL JRNL TITL 3 OF FREE UBIQUITIN. JRNL REF J.MOL.BIOL. V. 370 290 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17512543 JRNL DOI 10.1016/J.JMB.2007.04.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, XPLOR-NIH 2.9.7 REMARK 3 AUTHORS : DELAGLIO, F. (NMRPIPE), SCHWIETERS, C.D. (XPLOR REMARK 3 -NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURE WAS CALCULTATED USING REMARK 3 TORSION ANGLE DYNAMICS BY CYANA, FOLLOWED THE WATER REFINMENT REMARK 3 WITH XPLOR-NIH REMARK 4 REMARK 4 2I50 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039144. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM U-15N,13C, 25 MM SODIUM REMARK 210 PHOSPHATE, 100 MM KCL, 95% H2O, REMARK 210 5% D2O; 1MM U-15N, 25 MM SODIUM REMARK 210 PHOSPHATE, 100 MM KCL, 95% H2O, REMARK 210 5% D2O; 1MM U-15N, 13C, 25 MM REMARK 210 SODIUM PHOSPHATE, 100 MM KCL, REMARK 210 100% D2O; UNLABELED, 25 MM REMARK 210 SODIUM PHOSPHATE, 100 MM KCL, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA; HN(CO)CA; HN(CA)CB; REMARK 210 HN(COCA)CB; HNCO; HN(CA)CO; HNHA; REMARK 210 HCCH-TOCSY; 3D_15N-SEPARATED_ REMARK 210 NOESY; 3D_13C-SEPARATED_NOESY; REMARK 210 2D NOESY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA/XEASY 1.5.1, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 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 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 CYS A 31 102.93 -55.25 REMARK 500 1 ASP A 42 -73.94 -75.59 REMARK 500 1 ALA A 44 98.90 179.59 REMARK 500 1 GLU A 49 76.40 46.89 REMARK 500 2 CYS A 31 106.47 -55.31 REMARK 500 2 ALA A 44 126.32 174.22 REMARK 500 2 GLU A 46 -80.55 -49.60 REMARK 500 2 GLU A 47 -62.72 161.15 REMARK 500 2 GLU A 50 -155.17 65.94 REMARK 500 3 CYS A 31 105.07 -50.22 REMARK 500 3 ASN A 38 -133.84 56.55 REMARK 500 3 LYS A 39 -54.19 72.25 REMARK 500 3 GLU A 45 81.64 57.99 REMARK 500 3 THR A 48 -150.59 -146.71 REMARK 500 4 VAL A 6 143.14 57.23 REMARK 500 4 CYS A 31 106.58 -57.29 REMARK 500 4 GLU A 45 19.85 59.21 REMARK 500 4 GLU A 47 -50.72 -160.21 REMARK 500 4 GLU A 49 -167.55 -160.63 REMARK 500 4 GLU A 50 85.26 67.58 REMARK 500 4 PRO A 81 96.77 -69.47 REMARK 500 5 CYS A 31 108.34 -45.87 REMARK 500 5 ASN A 38 -30.93 74.79 REMARK 500 5 ASP A 42 -103.42 -38.71 REMARK 500 5 LYS A 43 -34.73 71.97 REMARK 500 5 THR A 48 96.34 -160.14 REMARK 500 5 ASP A 93 -62.80 -104.33 REMARK 500 5 TRP A 95 60.98 63.79 REMARK 500 6 CYS A 31 104.03 -54.52 REMARK 500 6 GLU A 46 103.35 -38.21 REMARK 500 6 GLU A 47 -57.53 -135.15 REMARK 500 6 TYR A 108 177.94 49.92 REMARK 500 7 CYS A 31 102.30 -53.69 REMARK 500 7 ASP A 37 93.64 -68.31 REMARK 500 7 HIS A 86 45.90 -80.71 REMARK 500 8 CYS A 31 105.86 -57.18 REMARK 500 8 GLU A 45 78.88 65.27 REMARK 500 8 GLU A 49 33.38 -97.97 REMARK 500 8 PRO A 81 45.59 -83.76 REMARK 500 8 SER A 83 -82.15 47.17 REMARK 500 8 TRP A 95 62.54 60.71 REMARK 500 8 TYR A 108 173.41 51.58 REMARK 500 9 CYS A 31 104.58 -55.80 REMARK 500 9 ASN A 38 -148.53 56.21 REMARK 500 9 LYS A 39 -69.74 64.01 REMARK 500 9 GLU A 46 -40.49 50.88 REMARK 500 9 THR A 48 48.38 -105.09 REMARK 500 9 CYS A 109 173.10 179.78 REMARK 500 9 SER A 111 76.98 70.65 REMARK 500 10 CYS A 31 108.40 -55.00 REMARK 500 REMARK 500 THIS ENTRY HAS 140 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 338 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 7 SG REMARK 620 2 HIS A 9 ND1 108.1 REMARK 620 3 CYS A 99 SG 109.1 107.4 REMARK 620 4 CYS A 102 SG 113.5 110.3 108.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 31 SG REMARK 620 2 CYS A 34 SG 106.8 REMARK 620 3 CYS A 65 SG 108.4 112.4 REMARK 620 4 HIS A 73 ND1 109.0 114.4 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 337 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 57 SG REMARK 620 2 CYS A 60 SG 104.7 REMARK 620 3 HIS A 77 NE2 107.9 111.7 REMARK 620 4 HIS A 86 ND1 108.3 111.9 111.9 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DEFINED 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 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 338 DBREF 2I50 A 5 126 UNP Q9Y5T5 UBP16_HUMAN 22 143 SEQADV 2I50 GLY A 1 UNP Q9Y5T5 CLONING ARTIFACT SEQADV 2I50 SER A 2 UNP Q9Y5T5 CLONING ARTIFACT SEQADV 2I50 HIS A 3 UNP Q9Y5T5 CLONING ARTIFACT SEQADV 2I50 MET A 4 UNP Q9Y5T5 CLONING ARTIFACT SEQRES 1 A 126 GLY SER HIS MET PRO VAL CYS ARG HIS ILE ARG LYS GLY SEQRES 2 A 126 LEU GLU GLN GLY ASN LEU LYS LYS ALA LEU VAL ASN VAL SEQRES 3 A 126 GLU TRP ASN ILE CYS GLN ASP CYS LYS THR ASP ASN LYS SEQRES 4 A 126 VAL LYS ASP LYS ALA GLU GLU GLU THR GLU GLU LYS PRO SEQRES 5 A 126 SER VAL TRP LEU CYS LEU LYS CYS GLY HIS GLN GLY CYS SEQRES 6 A 126 GLY ARG ASN SER GLN GLU GLN HIS ALA LEU LYS HIS TYR SEQRES 7 A 126 LEU THR PRO ARG SER GLU PRO HIS CYS LEU VAL LEU SER SEQRES 8 A 126 LEU ASP ASN TRP SER VAL TRP CYS TYR VAL CYS ASP ASN SEQRES 9 A 126 GLU VAL GLN TYR CYS SER SER ASN GLN LEU GLY GLN VAL SEQRES 10 A 126 VAL ASP TYR VAL ARG LYS GLN ALA SER HET ZN A 336 1 HET ZN A 337 1 HET ZN A 338 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 1 GLN A 16 LEU A 23 1 8 HELIX 2 2 GLN A 32 LYS A 35 1 4 HELIX 3 3 HIS A 73 LEU A 79 1 7 HELIX 4 4 GLN A 113 ALA A 125 1 13 SHEET 1 A 5 GLN A 63 CYS A 65 0 SHEET 2 A 5 VAL A 54 CYS A 57 -1 N TRP A 55 O GLY A 64 SHEET 3 A 5 LEU A 88 SER A 91 -1 O LEU A 90 N LEU A 56 SHEET 4 A 5 VAL A 97 CYS A 99 -1 O TRP A 98 N VAL A 89 SHEET 5 A 5 ASN A 104 VAL A 106 -1 O ASN A 104 N CYS A 99 LINK SG CYS A 7 ZN ZN A 338 1555 1555 2.34 LINK ND1 HIS A 9 ZN ZN A 338 1555 1555 2.09 LINK SG CYS A 31 ZN ZN A 336 1555 1555 2.29 LINK SG CYS A 34 ZN ZN A 336 1555 1555 2.29 LINK SG CYS A 57 ZN ZN A 337 1555 1555 2.33 LINK SG CYS A 60 ZN ZN A 337 1555 1555 2.30 LINK SG CYS A 65 ZN ZN A 336 1555 1555 2.31 LINK ND1 HIS A 73 ZN ZN A 336 1555 1555 2.05 LINK NE2 HIS A 77 ZN ZN A 337 1555 1555 2.12 LINK ND1 HIS A 86 ZN ZN A 337 1555 1555 2.09 LINK SG CYS A 99 ZN ZN A 338 1555 1555 2.35 LINK SG CYS A 102 ZN ZN A 338 1555 1555 2.28 SITE 1 AC1 4 CYS A 31 CYS A 34 CYS A 65 HIS A 73 SITE 1 AC2 4 CYS A 57 CYS A 60 HIS A 77 HIS A 86 SITE 1 AC3 4 CYS A 7 HIS A 9 CYS A 99 CYS A 102 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