HEADER HYDROLASE/SIGNALING PROTEIN 19-DEC-11 3V6C TITLE CRYSTAL STRUCTURE OF USP2 IN COMPLEX WITH MUTATED UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 41 KDA UBIQUITIN-SPECIFIC PROTEASE, DEUBIQUITINATING ENZYME COMPND 5 2, UBIQUITIN THIOLESTERASE 2, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE COMPND 6 2; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: 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, USP02.258.605, 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: PET28LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: 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: PET53 KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, UBIQUITIN, KEYWDS 2 PROTEASE, HYDROLASE-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.NECULAI,A.ERNST,S.SIDHU,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA, AUTHOR 2 J.WEIGELT,S.DHE-PAGANON,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 13-SEP-23 3V6C 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3V6C 1 REMARK REVDAT 2 14-AUG-13 3V6C 1 COMPND REVDAT 1 19-DEC-12 3V6C 0 JRNL AUTH M.NECULAI,A.ERNST,S.SIDHU,C.H.ARROWSMITH,A.M.EDWARDS, JRNL AUTH 2 C.BOUNTRA,J.WEIGELT,S.DHE-PAGANON JRNL TITL CRYSTAL STRUCTURE OF USP2 IN COMPLEX WITH MUTATED UBIQUITIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 43314 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2300 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2344 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.79000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 1.95000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.067 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3626 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4940 ; 1.983 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 470 ; 6.177 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;31.232 ;22.989 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;14.380 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;22.924 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2784 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 785 ; 0.002 ; 0.020 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): 2164 ; 0.876 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 863 ; 0.202 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3541 ; 1.544 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1465 ; 2.054 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1369 ; 3.329 ; 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): NULL ; NULL ; NULL 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 54.3837 43.1227 9.6740 REMARK 3 T TENSOR REMARK 3 T11: 0.0205 T22: 0.0249 REMARK 3 T33: 0.0045 T12: -0.0024 REMARK 3 T13: -0.0042 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.3640 L22: 0.2269 REMARK 3 L33: 0.0914 L12: -0.0146 REMARK 3 L13: 0.0292 L23: 0.0439 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.0122 S13: 0.0268 REMARK 3 S21: -0.0062 S22: 0.0003 S23: 0.0090 REMARK 3 S31: -0.0100 S32: 0.0041 S33: 0.0119 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 -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 62.4883 25.8643 12.5007 REMARK 3 T TENSOR REMARK 3 T11: 0.0339 T22: 0.0146 REMARK 3 T33: 0.0102 T12: -0.0009 REMARK 3 T13: 0.0068 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.9214 L22: 0.3723 REMARK 3 L33: 0.1332 L12: -0.2834 REMARK 3 L13: 0.1266 L23: 0.0206 REMARK 3 S TENSOR REMARK 3 S11: -0.0174 S12: 0.0393 S13: -0.0409 REMARK 3 S21: 0.0016 S22: 0.0166 S23: -0.0051 REMARK 3 S31: 0.0435 S32: 0.0090 S33: 0.0008 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3V6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45718 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 84.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.390 REMARK 200 R MERGE (I) : 0.05790 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.310 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: PDB ENTRY 2HD5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350,0.2 M CACL, 0.1 BIS-TRIS REMARK 280 PH 7.0, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.86750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.45750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.03850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.45750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.86750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.03850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 239 REMARK 465 GLY A 240 REMARK 465 SER A 241 REMARK 465 SER A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 SER A 249 REMARK 465 SER A 250 REMARK 465 GLY A 251 REMARK 465 LEU A 252 REMARK 465 VAL A 253 REMARK 465 PRO A 254 REMARK 465 ARG A 255 REMARK 465 GLY A 256 REMARK 465 SER A 257 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 SER A 382 REMARK 465 ASN A 383 REMARK 465 ARG A 448 REMARK 465 GLY A 449 REMARK 465 TYR A 450 REMARK 465 ARG A 509 REMARK 465 ILE A 510 REMARK 465 ARG A 511 REMARK 465 THR A 536 REMARK 465 ASN A 537 REMARK 465 SER A 600 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 465 MET B -16 REMARK 465 ALA B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 SER B -8 REMARK 465 SER B -7 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 LYS A 381 CG CD CE NZ REMARK 470 ASP A 393 OD2 REMARK 470 ARG A 480 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 590 O HOH A 936 1.96 REMARK 500 NZ LYS A 496 O HOH A 1010 2.01 REMARK 500 O GLY A 568 O HOH A 1015 2.04 REMARK 500 OG1 THR A 553 O HOH A 916 2.04 REMARK 500 NH2 ARG A 302 O HOH A 1017 2.04 REMARK 500 NH2 ARG A 563 O HOH A 918 2.14 REMARK 500 OG1 THR A 552 O HOH A 915 2.16 REMARK 500 O HOH A 1014 O HOH A 1025 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG B -2 O HOH A 904 3745 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 557 CG HIS A 557 CD2 0.059 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 349 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 504 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 504 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 563 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 563 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 587 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 587 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 LEU B 73 CB - CG - CD1 ANGL. DEV. = -10.6 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 ASN A 309 -165.79 -123.12 REMARK 500 ALA A 313 46.93 -96.57 REMARK 500 ASP A 427 -64.57 -92.05 REMARK 500 ASP A 575 -120.49 50.59 REMARK 500 TYR A 592 -46.37 -130.73 REMARK 500 LEU B 71 -145.39 -108.39 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 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 425 SG REMARK 620 2 CYS A 428 SG 108.2 REMARK 620 3 CYS A 476 SG 106.7 107.7 REMARK 620 4 CYS A 479 SG 109.5 110.3 114.2 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 CL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 101 DBREF 3V6C A 258 605 UNP O75604 UBP2_HUMAN 258 605 DBREF 3V6C B -2 74 UNP P0CG48 UBC_HUMAN 74 150 SEQADV 3V6C MET A 239 UNP O75604 EXPRESSION TAG SEQADV 3V6C GLY A 240 UNP O75604 EXPRESSION TAG SEQADV 3V6C SER A 241 UNP O75604 EXPRESSION TAG SEQADV 3V6C SER A 242 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 243 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 244 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 245 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 246 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 247 UNP O75604 EXPRESSION TAG SEQADV 3V6C HIS A 248 UNP O75604 EXPRESSION TAG SEQADV 3V6C SER A 249 UNP O75604 EXPRESSION TAG SEQADV 3V6C SER A 250 UNP O75604 EXPRESSION TAG SEQADV 3V6C GLY A 251 UNP O75604 EXPRESSION TAG SEQADV 3V6C LEU A 252 UNP O75604 EXPRESSION TAG SEQADV 3V6C VAL A 253 UNP O75604 EXPRESSION TAG SEQADV 3V6C PRO A 254 UNP O75604 EXPRESSION TAG SEQADV 3V6C ARG A 255 UNP O75604 EXPRESSION TAG SEQADV 3V6C GLY A 256 UNP O75604 EXPRESSION TAG SEQADV 3V6C SER A 257 UNP O75604 EXPRESSION TAG SEQADV 3V6C MET B -16 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C ALA B -15 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -14 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -13 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -12 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -11 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -10 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C HIS B -9 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C SER B -8 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C SER B -7 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C GLY B -6 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C LEU B -5 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C VAL B -4 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C PRO B -3 UNP P0CG48 EXPRESSION TAG SEQADV 3V6C SER B 0 UNP P0CG48 GLY 76 ENGINEERED MUTATION SEQADV 3V6C ASN B 6 UNP P0CG48 LYS 82 ENGINEERED MUTATION SEQADV 3V6C THR B 11 UNP P0CG48 LYS 87 ENGINEERED MUTATION SEQADV 3V6C HIS B 12 UNP P0CG48 THR 88 ENGINEERED MUTATION SEQRES 1 A 367 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 367 LEU VAL PRO ARG GLY SER MET ASN SER LYS SER ALA GLN SEQRES 3 A 367 GLY LEU ALA GLY LEU ARG ASN LEU GLY ASN THR CYS PHE SEQRES 4 A 367 MET ASN SER ILE LEU GLN CYS LEU SER ASN THR ARG GLU SEQRES 5 A 367 LEU ARG ASP TYR CYS LEU GLN ARG LEU TYR MET ARG ASP SEQRES 6 A 367 LEU HIS HIS GLY SER ASN ALA HIS THR ALA LEU VAL GLU SEQRES 7 A 367 GLU PHE ALA LYS LEU ILE GLN THR ILE TRP THR SER SER SEQRES 8 A 367 PRO ASN ASP VAL VAL SER PRO SER GLU PHE LYS THR GLN SEQRES 9 A 367 ILE GLN ARG TYR ALA PRO ARG PHE VAL GLY TYR ASN GLN SEQRES 10 A 367 GLN ASP ALA GLN GLU PHE LEU ARG PHE LEU LEU ASP GLY SEQRES 11 A 367 LEU HIS ASN GLU VAL ASN ARG VAL THR LEU ARG PRO LYS SEQRES 12 A 367 SER ASN PRO GLU ASN LEU ASP HIS LEU PRO ASP ASP GLU SEQRES 13 A 367 LYS GLY ARG GLN MET TRP ARG LYS TYR LEU GLU ARG GLU SEQRES 14 A 367 ASP SER ARG ILE GLY ASP LEU PHE VAL GLY GLN LEU LYS SEQRES 15 A 367 SER SER LEU THR CYS THR ASP CYS GLY TYR CYS SER THR SEQRES 16 A 367 VAL PHE ASP PRO PHE TRP ASP LEU SER LEU PRO ILE ALA SEQRES 17 A 367 LYS ARG GLY TYR PRO GLU VAL THR LEU MET ASP CYS MET SEQRES 18 A 367 ARG LEU PHE THR LYS GLU ASP VAL LEU ASP GLY ASP GLU SEQRES 19 A 367 LYS PRO THR CYS CYS ARG CYS ARG GLY ARG LYS ARG CYS SEQRES 20 A 367 ILE LYS LYS PHE SER ILE GLN ARG PHE PRO LYS ILE LEU SEQRES 21 A 367 VAL LEU HIS LEU LYS ARG PHE SER GLU SER ARG ILE ARG SEQRES 22 A 367 THR SER LYS LEU THR THR PHE VAL ASN PHE PRO LEU ARG SEQRES 23 A 367 ASP LEU ASP LEU ARG GLU PHE ALA SER GLU ASN THR ASN SEQRES 24 A 367 HIS ALA VAL TYR ASN LEU TYR ALA VAL SER ASN HIS SER SEQRES 25 A 367 GLY THR THR MET GLY GLY HIS TYR THR ALA TYR CYS ARG SEQRES 26 A 367 SER PRO GLY THR GLY GLU TRP HIS THR PHE ASN ASP SER SEQRES 27 A 367 SER VAL THR PRO MET SER SER SER GLN VAL ARG THR SER SEQRES 28 A 367 ASP ALA TYR LEU LEU PHE TYR GLU LEU ALA SER PRO PRO SEQRES 29 A 367 SER ARG MET SEQRES 1 B 91 MET ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL SEQRES 2 B 91 PRO ARG GLY SER MET GLN ILE PHE VAL ASN THR LEU THR SEQRES 3 B 91 GLY THR HIS ILE THR LEU GLU VAL GLU PRO SER ASP THR SEQRES 4 B 91 ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY SEQRES 5 B 91 ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS SEQRES 6 B 91 GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE SEQRES 7 B 91 GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG HET CL A 701 1 HET GOL A 702 6 HET ZN A 703 1 HET CL B 101 1 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CL 2(CL 1-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 ZN ZN 2+ FORMUL 7 HOH *290(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 LEU A 299 LEU A 304 1 6 HELIX 4 4 ALA A 313 TRP A 326 1 14 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 THR A 454 THR A 463 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 SER A 421 O VAL A 434 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 LEU A 468 O CYS A 485 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 SER A 550 -1 N ALA A 545 O PHE A 595 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 SER A 550 -1 N ALA A 545 O PHE A 595 SHEET 5 D 7 HIS A 557 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 PHE A 505 SER A 506 0 SHEET 2 E 2 SER A 513 LYS A 514 -1 O SER A 513 N SER A 506 SHEET 1 F 5 HIS B 12 VAL B 17 0 SHEET 2 F 5 MET B 1 ASN B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 F 5 THR B 66 VAL B 70 1 O LEU B 67 N ASN B 6 SHEET 4 F 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 F 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS A 425 ZN ZN A 703 1555 1555 2.40 LINK SG CYS A 428 ZN ZN A 703 1555 1555 2.37 LINK SG CYS A 476 ZN ZN A 703 1555 1555 2.31 LINK SG CYS A 479 ZN ZN A 703 1555 1555 2.37 SITE 1 AC1 6 THR A 454 LEU A 455 MET A 456 ASN A 520 SITE 2 AC1 6 PRO A 522 HOH A 867 SITE 1 AC2 8 ARG A 363 ASP A 367 HIS A 370 TRP A 439 SITE 2 AC2 8 HOH A 966 GLY B 47 LYS B 48 HOH B 208 SITE 1 AC3 4 CYS A 425 CYS A 428 CYS A 476 CYS A 479 SITE 1 AC4 4 ARG A 349 HOH A 865 ASP B 52 HOH B 210 CRYST1 57.735 84.077 86.915 90.00 90.00 90.00 P 21 21 21 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 0.017321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011505 0.00000