PDB Short entry for 2FOO HEADER HYDROLASE 13-JAN-06 2FOO TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HAUSP/USP7 COMPLEXED TITLE 2 WITH P53 PEPTIDE 359-362 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATH DOMAIN; COMPND 5 SYNONYM: UBIQUITIN THIOLESTERASE 7, UBIQUITIN-SPECIFIC PROCESSING COMPND 6 PROTEASE 7, DEUBIQUITINATING ENZYME 7, HERPESVIRUS ASSOCIATED COMPND 7 UBIQUITIN-SPECIFIC PROTEASE; COMPND 8 EC: 3.1.2.15; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: P53 PEPTIDE; COMPND 12 CHAIN: B; COMPND 13 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; 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS MATH DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SARIDAKIS,Y.SHENG,F.SARKARI,S.DUAN,T.WU,C.H.ARROWSMITH,L.FRAPPIER REVDAT 5 30-AUG-23 2FOO 1 SEQADV REVDAT 4 21-DEC-16 2FOO 1 TITLE VERSN REVDAT 3 24-FEB-09 2FOO 1 VERSN REVDAT 2 28-MAR-06 2FOO 1 JRNL REVDAT 1 14-FEB-06 2FOO 0 JRNL AUTH Y.SHENG,V.SARIDAKIS,F.SARKARI,S.DUAN,T.WU,C.H.ARROWSMITH, JRNL AUTH 2 L.FRAPPIER JRNL TITL MOLECULAR RECOGNITION OF P53 AND MDM2 BY USP7/HAUSP JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 285 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16474402 JRNL DOI 10.1038/NSMB1067 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 504674.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.0 REMARK 3 NUMBER OF REFLECTIONS : 9378 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) : 0.203 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.200 REMARK 3 FREE R VALUE TEST SET COUNT : 578 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1033 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1176 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 2.12000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.22 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 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) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 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) : 1.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.410 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.350 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 38.44 REMARK 3 REMARK 3 NCS MODEL : NULL 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 : NULL REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9385 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: PDB ENTRY 1YY6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4K, 0.1 M TRIS, 0.2 M LITHIUM REMARK 280 SULFATE , PH 8.5, VAPOR DIFFUSION, HANGING DROP, 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 22.76450 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 11.38225 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 34.14675 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 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 HIS 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 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 -83.04 72.65 REMARK 500 ASP A 145 104.18 -162.30 REMARK 500 VAL A 203 -77.78 -117.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FOJ RELATED DB: PDB REMARK 900 RELATED ID: 1YZE RELATED DB: PDB REMARK 900 RELATED ID: 1YY6 RELATED DB: PDB REMARK 900 RELATED ID: 2FOP RELATED DB: PDB DBREF 2FOO A 54 205 UNP Q93009 UBP7_HUMAN 54 205 DBREF 2FOO B 358 363 PDB 2FOO 2FOO 358 363 SEQADV 2FOO GLY A 51 UNP Q93009 CLONING ARTIFACT SEQADV 2FOO SER A 52 UNP Q93009 CLONING ARTIFACT SEQADV 2FOO HIS A 53 UNP Q93009 CLONING ARTIFACT SEQRES 1 A 155 GLY SER HIS THR ALA GLU GLU ASP MET GLU ASP ASP THR SEQRES 2 A 155 SER TRP ARG SER GLU ALA THR PHE GLN PHE THR VAL GLU SEQRES 3 A 155 ARG PHE SER ARG LEU SER GLU SER VAL LEU SER PRO PRO SEQRES 4 A 155 CYS PHE VAL ARG ASN LEU PRO TRP LYS ILE MET VAL MET SEQRES 5 A 155 PRO ARG PHE TYR PRO ASP ARG PRO HIS GLN LYS SER VAL SEQRES 6 A 155 GLY PHE PHE LEU GLN CYS ASN ALA GLU SER ASP SER THR SEQRES 7 A 155 SER TRP SER CYS HIS ALA GLN ALA VAL LEU LYS ILE ILE SEQRES 8 A 155 ASN TYR ARG ASP ASP GLU LYS SER PHE SER ARG ARG ILE SEQRES 9 A 155 SER HIS LEU PHE PHE HIS LYS GLU ASN ASP TRP GLY PHE SEQRES 10 A 155 SER ASN PHE MET ALA TRP SER GLU VAL THR ASP PRO GLU SEQRES 11 A 155 LYS GLY PHE ILE ASP ASP ASP LYS VAL THR PHE GLU VAL SEQRES 12 A 155 PHE VAL GLN ALA ASP ALA PRO HIS GLY VAL ALA TRP SEQRES 1 B 6 GLU PRO GLY GLY SER ARG FORMUL 3 HOH *101(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 VAL A 92 O LEU A 95 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 PHE A 118 N MET A 100 SHEET 4 C 4 ASP A 164 ALA A 172 -1 O MET A 171 N VAL A 115 CRYST1 69.825 69.825 45.529 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 0.014322 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021964 0.00000