PDB Short entry for 4JJQ HEADER HYDROLASE 08-MAR-13 4JJQ TITLE CRYSTAL STRUCTURE OF USP7-NTD WITH AN E2 ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: USP7-NTD, UNP RESIDUES 54-205; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7, HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 6 SPECIFIC PROTEASE, UBIQUITIN THIOESTERASE 7, UBIQUITIN-SPECIFIC- COMPND 7 PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 E1; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: UNP RESIDUES 5-14; COMPND 15 SYNONYM: UBCH6, UBIQUITIN CARRIER PROTEIN E1, UBIQUITIN-PROTEIN COMPND 16 LIGASE E1; COMPND 17 EC: 6.3.2.19; COMPND 18 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: HAUSP, USP7, USP7/HAUSP; 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: SYNTHESIZED PEPTIDE KEYWDS DEUBIQUITINATING ENZYME, HYDROLASE, TRAF DOMAIN, UBE2E1 EXPDTA X-RAY DIFFRACTION AUTHOR V.SARIDAKIS REVDAT 3 20-SEP-23 4JJQ 1 SEQADV REVDAT 2 18-APR-18 4JJQ 1 JRNL REVDAT 1 01-MAY-13 4JJQ 0 JRNL AUTH F.SARKARI,K.WHEATON,A.LA DELFA,M.MOHAMED,F.SHAIKH,R.KHATUN, JRNL AUTH 2 C.H.ARROWSMITH,L.FRAPPIER,V.SARIDAKIS,Y.SHENG JRNL TITL UBIQUITIN-SPECIFIC PROTEASE 7 IS A REGULATOR OF JRNL TITL 2 UBIQUITIN-CONJUGATING ENZYME UBE2E1. JRNL REF J. BIOL. CHEM. V. 288 16975 2013 JRNL REFN ESSN 1083-351X JRNL PMID 23603909 JRNL DOI 10.1074/JBC.M113.469262 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 89284.830 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 15267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1188 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2148 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 172 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1157 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 36.24 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4JJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17000 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1YY6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 4000, 0.1 M TRIS PH 8.5 AND REMARK 280 0.2 M LITHIUM SULFATE , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.86650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.43325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.29975 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 51 REMARK 465 SER A 52 REMARK 465 MET A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 GLU A 56 REMARK 465 GLU A 57 REMARK 465 ASP A 58 REMARK 465 MET A 59 REMARK 465 GLU A 60 REMARK 465 ASP A 61 REMARK 465 ASP A 62 REMARK 465 TYR A 106 REMARK 465 PRO A 107 REMARK 465 ASP A 108 REMARK 465 ARG A 109 REMARK 465 PRO A 110 REMARK 465 HIS A 111 REMARK 465 ALA A 206 REMARK 465 SER A 207 REMARK 465 THR A 208 REMARK 465 SER A 209 REMARK 465 ASP B 9 REMARK 465 SER B 10 REMARK 465 ARG B 11 REMARK 465 SER B 16 REMARK 465 SER B 17 REMARK 465 SER B 18 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 LYS A 113 -80.24 63.17 REMARK 500 ASP A 145 105.49 -165.34 REMARK 500 VAL A 203 -75.76 -116.87 REMARK 500 SER B 13 -178.95 -171.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 4JJQ A 54 207 UNP Q93009 UBP7_HUMAN 54 207 DBREF 4JJQ B 9 18 UNP P51965 UB2E1_HUMAN 5 14 SEQADV 4JJQ GLY A 51 UNP Q93009 EXPRESSION TAG SEQADV 4JJQ SER A 52 UNP Q93009 EXPRESSION TAG SEQADV 4JJQ MET A 53 UNP Q93009 EXPRESSION TAG SEQADV 4JJQ ALA A 206 UNP Q93009 ASP 206 ENGINEERED MUTATION SEQADV 4JJQ THR A 208 UNP Q93009 EXPRESSION TAG SEQADV 4JJQ SER A 209 UNP Q93009 EXPRESSION TAG SEQRES 1 A 159 GLY SER MET THR ALA GLU GLU ASP MET GLU ASP ASP THR SEQRES 2 A 159 SER TRP ARG SER GLU ALA THR PHE GLN PHE THR VAL GLU SEQRES 3 A 159 ARG PHE SER ARG LEU SER GLU SER VAL LEU SER PRO PRO SEQRES 4 A 159 CYS PHE VAL ARG ASN LEU PRO TRP LYS ILE MET VAL MET SEQRES 5 A 159 PRO ARG PHE TYR PRO ASP ARG PRO HIS GLN LYS SER VAL SEQRES 6 A 159 GLY PHE PHE LEU GLN CYS ASN ALA GLU SER ASP SER THR SEQRES 7 A 159 SER TRP SER CYS HIS ALA GLN ALA VAL LEU LYS ILE ILE SEQRES 8 A 159 ASN TYR ARG ASP ASP GLU LYS SER PHE SER ARG ARG ILE SEQRES 9 A 159 SER HIS LEU PHE PHE HIS LYS GLU ASN ASP TRP GLY PHE SEQRES 10 A 159 SER ASN PHE MET ALA TRP SER GLU VAL THR ASP PRO GLU SEQRES 11 A 159 LYS GLY PHE ILE ASP ASP ASP LYS VAL THR PHE GLU VAL SEQRES 12 A 159 PHE VAL GLN ALA ASP ALA PRO HIS GLY VAL ALA TRP ALA SEQRES 13 A 159 SER THR SER SEQRES 1 B 10 ASP SER ARG ALA SER THR SER SER SER SER FORMUL 3 HOH *75(H2 O) HELIX 1 1 ARG A 77 LEU A 81 5 5 HELIX 2 2 ASP A 145 SER A 149 5 5 HELIX 3 3 TRP A 173 THR A 177 1 5 SHEET 1 A 4 GLU A 68 VAL A 75 0 SHEET 2 A 4 VAL A 189 ALA A 197 -1 O VAL A 189 N VAL A 75 SHEET 3 A 4 SER A 131 ILE A 140 -1 N LYS A 139 O GLU A 192 SHEET 4 A 4 PHE A 150 PHE A 159 -1 O ARG A 152 N LEU A 138 SHEET 1 B 3 VAL A 85 LEU A 86 0 SHEET 2 B 3 LEU A 95 ARG A 104 -1 O VAL A 101 N VAL A 85 SHEET 3 B 3 CYS A 90 VAL A 92 -1 N CYS A 90 O TRP A 97 SHEET 1 C 4 VAL A 85 LEU A 86 0 SHEET 2 C 4 LEU A 95 ARG A 104 -1 O VAL A 101 N VAL A 85 SHEET 3 C 4 SER A 114 CYS A 121 -1 O GLY A 116 N MET A 102 SHEET 4 C 4 ASP A 164 ALA A 172 -1 O TRP A 165 N LEU A 119 CRYST1 69.901 69.901 45.733 90.00 90.00 90.00 P 41 4 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 0.014306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021866 0.00000