HEADER HYDROLASE 29-MAR-11 2LBC TITLE SOLUTION STRUCTURE OF TANDEM UBA OF USP13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 652-777; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 13, ISOPEPTIDASE T-3, ISOT-3, COMPND 6 UBIQUITIN THIOLESTERASE 13, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE COMPND 7 13; COMPND 8 EC: 3.4.19.12; 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: USP13, ISOT3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-32M KEYWDS TANDEM UBA OF USP13, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.ZHANG,C.ZHOU,Z.ZHOU,A.SONG,H.HU REVDAT 3 15-MAY-24 2LBC 1 REMARK REVDAT 2 14-JUN-23 2LBC 1 REMARK REVDAT 1 07-MAR-12 2LBC 0 JRNL AUTH Y.ZHANG,C.ZHOU,Z.ZHOU,A.SONG,H.HU JRNL TITL DOMAIN ANALYSIS REVEALS THAT A DEUBIQUITINATING ENZYME USP13 JRNL TITL 2 PERFORMS NON-ACTIVATING CATALYSIS FOR LYS63-LINKED JRNL TITL 3 POLYUBIQUITIN. JRNL REF PLOS ONE V. 6 29362 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 22216260 JRNL DOI 10.1371/JOURNAL.PONE.0029362 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA2.0, ARIA2.0 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA2.0), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA2.0) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000102188. 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 : 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE-1, 50 MM REMARK 210 SODIUM CHLORIDE-2, 1 MM [U-100% REMARK 210 15N] ENTITY-3, 90% H2O/10% D2O; REMARK 210 20 MM SODIUM PHOSPHATE-4, 50 MM REMARK 210 SODIUM CHLORIDE-5, 1 MM [U-100% REMARK 210 13C; U-100% 15N] ENTITY-6, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D C(CO)NH; 3D HNHA; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 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, SPARKY, TALOS, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 ALA A 23 H THR A 27 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 GLU A 12 1.27 -69.53 REMARK 500 1 PRO A 16 80.79 -69.66 REMARK 500 1 ASN A 29 75.42 58.94 REMARK 500 1 GLU A 50 105.10 -41.76 REMARK 500 1 TYR A 57 75.23 -172.33 REMARK 500 1 ALA A 63 -61.26 -142.77 REMARK 500 1 SER A 71 102.86 65.37 REMARK 500 1 ASP A 74 162.35 70.20 REMARK 500 1 PRO A 77 167.05 -49.85 REMARK 500 1 ASN A 103 63.27 65.18 REMARK 500 1 ASN A 104 28.93 49.66 REMARK 500 1 PRO A 117 -70.08 -51.30 REMARK 500 1 GLU A 118 -57.97 -168.90 REMARK 500 1 GLU A 120 99.46 60.75 REMARK 500 1 SER A 123 32.47 -88.80 REMARK 500 1 PHE A 125 71.19 51.87 REMARK 500 2 ILE A 2 86.19 62.34 REMARK 500 2 ASP A 3 82.88 -67.92 REMARK 500 2 ALA A 49 -120.06 -84.42 REMARK 500 2 SER A 71 -65.79 70.23 REMARK 500 2 GLU A 118 -51.00 -166.89 REMARK 500 2 PHE A 119 37.43 -140.68 REMARK 500 2 GLU A 120 -178.96 68.27 REMARK 500 2 ASP A 122 132.62 73.30 REMARK 500 3 ASP A 3 81.15 -66.15 REMARK 500 3 ASN A 29 60.57 60.84 REMARK 500 3 GLU A 50 108.17 -47.08 REMARK 500 3 LEU A 52 31.56 -96.98 REMARK 500 3 ALA A 60 -72.19 67.51 REMARK 500 3 ALA A 61 -62.50 -99.48 REMARK 500 3 ALA A 65 -48.25 -171.76 REMARK 500 3 ASN A 103 60.03 63.81 REMARK 500 3 GLU A 118 -39.60 -177.67 REMARK 500 3 ASP A 122 72.40 54.36 REMARK 500 3 ASP A 124 -78.53 -47.15 REMARK 500 4 MET A 13 32.47 -92.14 REMARK 500 4 PRO A 16 91.44 -55.10 REMARK 500 4 LEU A 17 57.32 -96.81 REMARK 500 4 ALA A 49 -123.82 -93.21 REMARK 500 4 THR A 53 72.83 37.01 REMARK 500 4 ALA A 60 -164.53 -125.37 REMARK 500 4 SER A 66 -159.20 -161.31 REMARK 500 4 GLU A 118 -60.94 -169.81 REMARK 500 4 PHE A 119 28.46 -152.56 REMARK 500 4 GLU A 120 -154.45 65.10 REMARK 500 4 GLU A 121 -167.94 -73.86 REMARK 500 5 LEU A 17 57.66 -94.20 REMARK 500 5 ASN A 29 73.91 60.67 REMARK 500 5 GLU A 44 2.56 -69.63 REMARK 500 5 ALA A 49 -92.72 -81.87 REMARK 500 REMARK 500 THIS ENTRY HAS 161 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17554 RELATED DB: BMRB DBREF 2LBC A 1 126 UNP Q92995 UBP13_HUMAN 652 777 SEQRES 1 A 126 ASP ILE ASP GLU SER SER VAL MET GLN LEU ALA GLU MET SEQRES 2 A 126 GLY PHE PRO LEU GLU ALA CYS ARG LYS ALA VAL TYR PHE SEQRES 3 A 126 THR GLY ASN MET GLY ALA GLU VAL ALA PHE ASN TRP ILE SEQRES 4 A 126 ILE VAL HIS MET GLU GLU PRO ASP PHE ALA GLU PRO LEU SEQRES 5 A 126 THR MET PRO GLY TYR GLY GLY ALA ALA SER ALA GLY ALA SEQRES 6 A 126 SER VAL PHE GLY ALA SER GLY LEU ASP ASN GLN PRO PRO SEQRES 7 A 126 GLU GLU ILE VAL ALA ILE ILE THR SER MET GLY PHE GLN SEQRES 8 A 126 ARG ASN GLN ALA ILE GLN ALA LEU ARG ALA THR ASN ASN SEQRES 9 A 126 ASN LEU GLU ARG ALA LEU ASP TRP ILE PHE SER HIS PRO SEQRES 10 A 126 GLU PHE GLU GLU ASP SER ASP PHE VAL HELIX 1 1 GLU A 4 GLU A 12 1 9 HELIX 2 2 LEU A 17 GLY A 28 1 12 HELIX 3 3 GLY A 31 HIS A 42 1 12 HELIX 4 4 MET A 43 GLU A 45 5 3 HELIX 5 5 PRO A 78 GLY A 89 1 12 HELIX 6 6 GLN A 91 ASN A 103 1 13 HELIX 7 7 ASN A 105 SER A 115 1 11 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