HEADER HYDROLASE 14-DEC-05 2DAG TITLE SOLUTION STRUCTURE OF THE FIRST UBA DOMAIN IN THE HUMAN UBIQUITIN TITLE 2 SPECIFIC PROTEASE 5 (ISOPEPTIDASE 5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBA DOMAIN; COMPND 5 SYNONYM: UBIQUITIN THIOLESTERASE 5, UBIQUITIN-SPECIFIC PROCESSING COMPND 6 PROTEASE 5, DEUBIQUITINATING ENZYME 5, ISOPEPTIDASE T; COMPND 7 EC: 3.1.2.15; 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: USP5; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050613-08; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ISOPEPTIDASE T, UBIQUITIN SPECIFIC PROTEASE 5 (USP 5), UBA DOMAIN, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.ZHAO,T.KIGAWA,T.TOMIZAWA,S.KOSHIBA,M.INOUE,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 29-MAY-24 2DAG 1 REMARK REVDAT 3 09-MAR-22 2DAG 1 REMARK SEQADV REVDAT 2 24-FEB-09 2DAG 1 VERSN REVDAT 1 14-JUN-06 2DAG 0 JRNL AUTH C.ZHAO,T.KIGAWA,T.TOMIZAWA,S.KOSHIBA,M.INOUE,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST UBA DOMAIN IN THE HUMAN JRNL TITL 2 UBIQUITIN SPECIFIC PROTEASE 5 (ISOPEPTIDASE 5) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 1.0.8 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DAG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025183. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.05MM UBA DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9321, CYANA 1.0.8 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS 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 ALA A 38 H MET A 42 1.51 REMARK 500 O HIS A 48 H ASP A 51 1.51 REMARK 500 O MET A 42 H MET A 46 1.57 REMARK 500 O GLU A 10 H ILE A 14 1.59 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 3 92.81 -59.74 REMARK 500 1 SER A 5 -61.93 69.97 REMARK 500 1 SER A 6 157.23 64.68 REMARK 500 1 LEU A 8 167.94 55.70 REMARK 500 1 TYR A 31 -70.89 -48.33 REMARK 500 1 ASN A 35 98.20 50.86 REMARK 500 1 SER A 36 46.96 -148.39 REMARK 500 1 ASN A 56 155.96 -40.55 REMARK 500 1 SER A 69 -60.97 -129.22 REMARK 500 2 SER A 3 138.78 -173.33 REMARK 500 2 TYR A 31 -71.05 -50.99 REMARK 500 2 ASN A 35 94.39 47.52 REMARK 500 2 SER A 36 54.79 -143.79 REMARK 500 2 ASP A 50 44.31 -88.85 REMARK 500 2 ILE A 59 109.61 58.18 REMARK 500 2 SER A 63 85.30 -154.53 REMARK 500 2 SER A 64 95.01 -65.12 REMARK 500 2 SER A 68 -61.52 -156.84 REMARK 500 2 SER A 69 153.25 -49.06 REMARK 500 2 SER A 72 80.80 -177.68 REMARK 500 2 SER A 73 88.95 62.15 REMARK 500 3 ALA A 29 -70.16 -54.16 REMARK 500 3 HIS A 48 -62.49 -91.95 REMARK 500 3 ASN A 56 157.36 -40.52 REMARK 500 3 SER A 63 -61.69 -150.47 REMARK 500 3 SER A 68 162.31 60.13 REMARK 500 4 SER A 2 119.52 -174.40 REMARK 500 4 SER A 3 -60.95 71.30 REMARK 500 4 SER A 5 -62.57 -103.79 REMARK 500 4 SER A 6 91.45 51.85 REMARK 500 4 ASN A 35 85.59 40.24 REMARK 500 4 MET A 46 -30.67 -37.94 REMARK 500 4 ASP A 50 42.43 -90.71 REMARK 500 4 ASN A 56 157.33 -40.97 REMARK 500 4 PRO A 57 -169.09 -75.08 REMARK 500 4 LEU A 60 160.38 -46.39 REMARK 500 4 SER A 72 105.55 -55.27 REMARK 500 4 SER A 73 151.70 61.89 REMARK 500 5 SER A 5 -58.47 -142.34 REMARK 500 5 SER A 68 134.15 64.91 REMARK 500 5 SER A 72 -58.92 -130.18 REMARK 500 6 SER A 2 103.30 -56.00 REMARK 500 6 SER A 3 101.86 54.78 REMARK 500 6 SER A 5 112.43 61.18 REMARK 500 6 ALA A 29 -70.67 -55.03 REMARK 500 6 ASN A 35 89.60 40.70 REMARK 500 6 ILE A 59 140.28 62.05 REMARK 500 6 LEU A 60 161.24 -45.27 REMARK 500 6 SER A 72 -58.47 -144.77 REMARK 500 7 SER A 5 146.60 -170.07 REMARK 500 REMARK 500 THIS ENTRY HAS 159 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002005673.1 RELATED DB: TARGETDB DBREF 2DAG A 8 68 UNP P45974 UBP5_HUMAN 655 715 SEQADV 2DAG GLY A 1 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 2 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 3 UNP P45974 CLONING ARTIFACT SEQADV 2DAG GLY A 4 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 5 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 6 UNP P45974 CLONING ARTIFACT SEQADV 2DAG GLY A 7 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 69 UNP P45974 CLONING ARTIFACT SEQADV 2DAG GLY A 70 UNP P45974 CLONING ARTIFACT SEQADV 2DAG PRO A 71 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 72 UNP P45974 CLONING ARTIFACT SEQADV 2DAG SER A 73 UNP P45974 CLONING ARTIFACT SEQADV 2DAG GLY A 74 UNP P45974 CLONING ARTIFACT SEQRES 1 A 74 GLY SER SER GLY SER SER GLY LEU ASP GLU SER VAL ILE SEQRES 2 A 74 ILE GLN LEU VAL GLU MET GLY PHE PRO MET ASP ALA CYS SEQRES 3 A 74 ARG LYS ALA VAL TYR TYR THR GLY ASN SER GLY ALA GLU SEQRES 4 A 74 ALA ALA MET ASN TRP VAL MET SER HIS MET ASP ASP PRO SEQRES 5 A 74 ASP PHE ALA ASN PRO LEU ILE LEU PRO GLY SER SER GLY SEQRES 6 A 74 PRO GLY SER SER GLY PRO SER SER GLY HELIX 1 1 ASP A 9 GLY A 20 1 12 HELIX 2 2 PRO A 22 GLY A 34 1 13 HELIX 3 3 GLY A 37 MET A 49 1 13 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