PDB Short entry for 3NHE HEADER HYDROLASE/PROTEIN BINDING 14-JUN-10 3NHE TITLE HIGH RESOLUTION STRUCTURE (1.26A) OF USP2A IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 258-605; COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 2, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 2, DEUBIQUITINATING ENZYME 2, 41 KDA UBIQUITIN-SPECIFIC COMPND 7 PROTEASE; COMPND 8 EC: 3.1.2.15; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UBIQUITIN; 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: UBP41, USP2; 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: PET24A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RPS27A, UBA52, UBB, UBC; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTBY2 KEYWDS DEUBIQUITINATING PROTEASE, CYSTEINE PROTEASE, SUBSTRATE ENZYME KEYWDS 2 COMPLEX, HYDROLASE-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,L.J.DELUCAS,D.POWELL MCCOMBS REVDAT 2 06-SEP-23 3NHE 1 REMARK LINK REVDAT 1 30-JUN-10 3NHE 0 JRNL AUTH N.SCHORMANN,D.POWELL MCCOMBS,L.J.DELUCAS JRNL TITL HIGH RESOLUTION STRUCTURE OF USP2A IN COMPLEX WITH UBIQUITIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 97957 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 + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5146 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.26 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6350 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 337 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3334 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 508 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.397 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3510 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4764 ; 1.036 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 5.633 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;30.163 ;23.046 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 637 ;10.470 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;14.433 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 524 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2690 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2119 ; 0.609 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3449 ; 1.143 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1391 ; 1.519 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1299 ; 2.446 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3510 ; 0.671 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 263 A 600 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7980 -1.9770 16.9480 REMARK 3 T TENSOR REMARK 3 T11: 0.0093 T22: 0.0080 REMARK 3 T33: 0.0013 T12: -0.0010 REMARK 3 T13: -0.0002 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.2799 L22: 0.1127 REMARK 3 L33: 0.0887 L12: 0.0626 REMARK 3 L13: -0.0243 L23: -0.0064 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: 0.0203 S13: 0.0051 REMARK 3 S21: -0.0039 S22: 0.0130 S23: -0.0022 REMARK 3 S31: 0.0095 S32: 0.0049 S33: -0.0003 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7920 8.3750 23.8960 REMARK 3 T TENSOR REMARK 3 T11: 0.0097 T22: 0.0026 REMARK 3 T33: 0.0047 T12: 0.0005 REMARK 3 T13: 0.0011 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.6759 L22: 0.2620 REMARK 3 L33: 0.2409 L12: -0.0294 REMARK 3 L13: -0.0184 L23: 0.0783 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: 0.0144 S13: 0.0421 REMARK 3 S21: 0.0056 S22: 0.0003 S23: 0.0179 REMARK 3 S31: -0.0177 S32: -0.0207 S33: 0.0101 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3NHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25800 REMARK 200 R SYM FOR SHELL (I) : 0.25800 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: PHASER REMARK 200 STARTING MODEL: 2HD5, 2IBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG4000, 0.1M HEPES, PH 7.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.38550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.98050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.38550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.98050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A 258 REMARK 465 ASN A 259 REMARK 465 SER A 260 REMARK 465 LYS A 261 REMARK 465 SER A 262 REMARK 465 PRO A 601 REMARK 465 PRO A 602 REMARK 465 SER A 603 REMARK 465 ARG A 604 REMARK 465 MET A 605 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 382 CB OG REMARK 470 ASN A 383 CB CG OD1 ND2 REMARK 470 PRO A 384 CG CD REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 554 CA CB CG SD CE REMARK 480 ARG B 74 N CA C O CB CG CD REMARK 480 ARG B 74 NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 384 N - CA - CB ANGL. DEV. = 7.3 DEGREES 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 SER A 308 95.12 -69.23 REMARK 500 ASN A 331 -8.48 84.00 REMARK 500 SER A 382 131.79 74.63 REMARK 500 ASP A 575 -111.82 41.49 REMARK 500 THR B 7 -157.09 -87.83 REMARK 500 LEU B 71 -145.44 -105.09 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 425 SG REMARK 620 2 CYS A 428 SG 108.1 REMARK 620 3 CYS A 476 SG 108.6 106.1 REMARK 620 4 CYS A 479 SG 110.2 109.1 114.4 REMARK 620 N 1 2 3 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 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HD5 RELATED DB: PDB REMARK 900 RELATED ID: 2IBI RELATED DB: PDB DBREF 3NHE A 258 605 UNP O75604 UBP2_HUMAN 258 605 DBREF 3NHE B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQRES 1 A 348 MET ASN SER LYS SER ALA GLN GLY LEU ALA GLY LEU ARG SEQRES 2 A 348 ASN LEU GLY ASN THR CME PHE MET ASN SER ILE LEU GLN SEQRES 3 A 348 CYS LEU SER ASN THR ARG GLU LEU ARG ASP TYR CYS LEU SEQRES 4 A 348 GLN ARG LEU TYR MET ARG ASP LEU HIS HIS GLY SER ASN SEQRES 5 A 348 ALA HIS THR ALA LEU VAL GLU GLU PHE ALA LYS LEU ILE SEQRES 6 A 348 GLN THR ILE TRP THR SER SER PRO ASN ASP VAL VAL SER SEQRES 7 A 348 PRO SER GLU PHE LYS THR GLN ILE GLN ARG TYR ALA PRO SEQRES 8 A 348 ARG PHE VAL GLY TYR ASN GLN GLN ASP ALA GLN GLU PHE SEQRES 9 A 348 LEU ARG PHE LEU LEU ASP GLY LEU HIS ASN GLU VAL ASN SEQRES 10 A 348 ARG VAL THR LEU ARG PRO LYS SER ASN PRO GLU ASN LEU SEQRES 11 A 348 ASP HIS LEU PRO ASP ASP GLU LYS GLY ARG GLN MET TRP SEQRES 12 A 348 ARG LYS TYR LEU GLU ARG GLU ASP SER ARG ILE GLY ASP SEQRES 13 A 348 LEU PHE VAL GLY GLN LEU LYS SER SER LEU THR CYS THR SEQRES 14 A 348 ASP CYS GLY TYR CYS SER THR VAL PHE ASP PRO PHE TRP SEQRES 15 A 348 ASP LEU SER LEU PRO ILE ALA LYS ARG GLY TYR PRO GLU SEQRES 16 A 348 VAL THR LEU MET ASP CYS MET ARG LEU PHE THR LYS GLU SEQRES 17 A 348 ASP VAL LEU ASP GLY ASP GLU LYS PRO THR CYS CYS ARG SEQRES 18 A 348 CYS ARG GLY ARG LYS ARG CYS ILE LYS LYS PHE SER ILE SEQRES 19 A 348 GLN ARG PHE PRO LYS ILE LEU VAL LEU HIS LEU LYS ARG SEQRES 20 A 348 PHE SER GLU SER ARG ILE ARG THR SER LYS LEU THR THR SEQRES 21 A 348 PHE VAL ASN PHE PRO LEU ARG ASP LEU ASP LEU ARG GLU SEQRES 22 A 348 PHE ALA SER GLU ASN THR ASN HIS ALA VAL TYR ASN LEU SEQRES 23 A 348 TYR ALA VAL SER ASN HIS SER GLY THR THR MET GLY GLY SEQRES 24 A 348 HIS TYR THR ALA TYR CYS ARG SER PRO GLY THR GLY GLU SEQRES 25 A 348 TRP HIS THR PHE ASN ASP SER SER VAL THR PRO MET SER SEQRES 26 A 348 SER SER GLN VAL ARG THR SER ASP ALA TYR LEU LEU PHE SEQRES 27 A 348 TYR GLU LEU ALA SER PRO PRO SER ARG MET SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MODRES 3NHE CME A 276 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 276 10 HET ZN A 1 1 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM ZN ZINC ION FORMUL 1 CME C5 H11 N O3 S2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *508(H2 O) HELIX 1 1 THR A 275 ASN A 287 1 13 HELIX 2 2 THR A 288 GLN A 297 1 10 HELIX 3 3 ARG A 298 ASP A 303 5 6 HELIX 4 4 HIS A 311 TRP A 326 1 16 HELIX 5 5 PRO A 336 ALA A 347 1 12 HELIX 6 6 PRO A 348 VAL A 351 5 4 HELIX 7 7 ASP A 357 ASN A 374 1 18 HELIX 8 8 PRO A 391 GLU A 405 1 15 HELIX 9 9 SER A 409 VAL A 416 1 8 HELIX 10 10 LEU A 455 LYS A 464 1 10 HELIX 11 11 ASP A 469 LYS A 473 5 5 HELIX 12 12 ARG A 529 ALA A 532 5 4 HELIX 13 13 SER A 582 VAL A 586 5 5 HELIX 14 14 THR B 22 GLY B 35 1 14 HELIX 15 15 PRO B 37 GLN B 41 5 5 HELIX 16 16 LEU B 56 ASN B 60 5 5 SHEET 1 A 2 GLY A 268 LEU A 269 0 SHEET 2 A 2 VAL A 333 VAL A 334 1 O VAL A 334 N GLY A 268 SHEET 1 B 4 CYS A 431 PHE A 438 0 SHEET 2 B 4 GLY A 417 CYS A 425 -1 N LEU A 419 O ASP A 436 SHEET 3 B 4 CYS A 485 ARG A 493 -1 O SER A 490 N LYS A 420 SHEET 4 B 4 ASP A 466 LEU A 468 -1 N ASP A 466 O LYS A 487 SHEET 1 C 5 LEU A 441 LEU A 443 0 SHEET 2 C 5 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 C 5 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 C 5 VAL A 540 GLY A 551 -1 N ASN A 542 O GLU A 597 SHEET 5 C 5 LEU A 526 ASP A 527 -1 N LEU A 526 O TYR A 541 SHEET 1 D 7 LEU A 441 LEU A 443 0 SHEET 2 D 7 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 D 7 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 D 7 VAL A 540 GLY A 551 -1 N ASN A 542 O GLU A 597 SHEET 5 D 7 GLY A 556 ARG A 563 -1 O ARG A 563 N TYR A 544 SHEET 6 D 7 TRP A 570 ASN A 574 -1 O PHE A 573 N ALA A 560 SHEET 7 D 7 SER A 577 MET A 581 -1 O SER A 577 N ASN A 574 SHEET 1 E 2 VAL A 453 THR A 454 0 SHEET 2 E 2 VAL A 519 ASN A 520 1 O ASN A 520 N VAL A 453 SHEET 1 F 2 THR A 475 CYS A 476 0 SHEET 2 F 2 GLY A 481 ARG A 482 -1 O GLY A 481 N CYS A 476 SHEET 1 G 5 THR B 12 GLU B 16 0 SHEET 2 G 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 G 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 G 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 G 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK C THR A 275 N CME A 276 1555 1555 1.33 LINK C CME A 276 N PHE A 277 1555 1555 1.33 LINK ZN ZN A 1 SG CYS A 425 1555 1555 2.33 LINK ZN ZN A 1 SG CYS A 428 1555 1555 2.35 LINK ZN ZN A 1 SG CYS A 476 1555 1555 2.28 LINK ZN ZN A 1 SG CYS A 479 1555 1555 2.35 CISPEP 1 TYR A 450 PRO A 451 0 10.32 SITE 1 AC1 4 CYS A 425 CYS A 428 CYS A 476 CYS A 479 CRYST1 102.771 53.961 74.719 90.00 107.71 90.00 C 1 2 1 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 0.009730 0.000000 0.003107 0.00000 SCALE2 0.000000 0.018532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014049 0.00000