HEADER LIGASE 17-APR-13 4K7S TITLE CRYSTAL STRUCTURE OF ZN2-HUB (HUMAN UBIQUITIN) ADDUCT FROM A SOLUTION TITLE 2 35 MM ZINC ACETATE/1.3 MM HUB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 1-73; COMPND 5 SYNONYM: POLYUBIQUITIN-C; COMPND 6 EC: 6.3.2.19; COMPND 7 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE, ZN ADDUCT EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.FALINI,M.CALVARESI,A.BOTTONI,F.ARNESANO,G.NATILE REVDAT 3 20-SEP-23 4K7S 1 REMARK LINK REVDAT 2 01-MAR-17 4K7S 1 JRNL REVDAT 1 08-MAY-13 4K7S 0 JRNL AUTH S.FERMANI,G.FALINI,M.CALVARESI,A.BOTTONI,V.CALO,V.MANGINI, JRNL AUTH 2 F.ARNESANO,G.NATILE JRNL TITL CONFORMATIONAL SELECTION OF UBIQUITIN QUATERNARY STRUCTURES JRNL TITL 2 DRIVEN BY ZINC IONS. JRNL REF CHEMISTRY V. 19 15480 2013 JRNL REFN ISSN 0947-6539 JRNL PMID 24123543 JRNL DOI 10.1002/CHEM.201302229 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.ARNESANO,B.D.BELVISO,R.CALIANDRO,G.FALINI,S.FERMANI, REMARK 1 AUTH 2 G.NATILE,D.SILIQI REMARK 1 TITL CRYSTALLOGRAPHIC ANALYSIS OF METAL-ION BINDING TO HUMAN REMARK 1 TITL 2 UBIQUITIN. REMARK 1 REF CHEMISTRY V. 17 1569 2011 REMARK 1 REFN ISSN 0947-6539 REMARK 1 PMID 21268159 REMARK 1 DOI 10.1002/CHEM.201001617 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.FALINI,S.FERMANI,G.TOSI,F.ARNESANO,G.NATILE REMARK 1 TITL STRUCTURAL PROBING OF ZN(II), CD(II) AND HG(II) BINDING TO REMARK 1 TITL 2 HUMAN UBIQUITIN. REMARK 1 REF CHEM.COMMUN.(CAMB.) V. 45 5960 2008 REMARK 1 REFN ISSN 1359-7345 REMARK 1 PMID 19030552 REMARK 1 DOI 10.1039/B813463D REMARK 2 REMARK 2 RESOLUTION. 1.76 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20239 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1471 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1703 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.28000 REMARK 3 B33 (A**2) : -0.25000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.390 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.846 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1796 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2429 ; 1.969 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 5.714 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;39.064 ;26.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 373 ;16.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.609 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 291 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1305 ; 0.010 ; 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): 1103 ; 1.154 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1812 ; 1.861 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 693 ; 3.345 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 607 ; 5.358 ; 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 : NULL 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 4K7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.26 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 34.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.24200 REMARK 200 R SYM (I) : 0.24200 REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : 0.32700 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 3EHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1450, 50MM HEPES PH 7.0, REMARK 280 35 MM ZINC ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 21.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.01500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.01500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.16500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 LEU A 71 REMARK 465 ARG A 72 REMARK 465 LEU A 73 REMARK 465 ARG A 74 REMARK 465 GLY A 75 REMARK 465 GLY A 76 REMARK 465 LEU B 73 REMARK 465 ARG B 74 REMARK 465 GLY B 75 REMARK 465 GLY B 76 REMARK 465 LEU C 73 REMARK 465 ARG C 74 REMARK 465 GLY C 75 REMARK 465 GLY C 76 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 O HOH A 298 O HOH A 300 1.82 REMARK 500 O HOH C 249 O HOH C 278 1.85 REMARK 500 OE1 GLU A 18 O HOH A 298 1.87 REMARK 500 O HOH C 227 O HOH C 316 1.96 REMARK 500 OG1 THR A 9 O HOH A 307 1.97 REMARK 500 O HOH C 246 O HOH C 290 1.98 REMARK 500 O HOH B 281 O HOH B 296 2.05 REMARK 500 C2 EDO A 103 O HOH A 300 2.10 REMARK 500 O HOH B 222 O HOH B 239 2.12 REMARK 500 OD1 ASP C 21 O HOH A 298 2.13 REMARK 500 O HOH C 231 O HOH C 232 2.14 REMARK 500 O HOH B 244 O HOH B 275 2.15 REMARK 500 O HOH A 302 O HOH B 280 2.17 REMARK 500 O HOH A 209 O HOH A 258 2.19 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 O HOH A 224 O HOH C 276 4555 2.15 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 GLU A 64 2.93 80.69 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 GLU A 16 OE1 96.7 REMARK 620 3 HOH C 223 O 87.2 110.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 EDO A 103 O1 99.4 REMARK 620 3 HOH A 299 O 117.3 116.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 HOH A 265 O 93.6 REMARK 620 3 HIS B 68 NE2 105.9 159.3 REMARK 620 4 HOH B 203 O 112.6 58.8 105.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 EDO A 103 O2 REMARK 620 2 GLU C 18 OE1 97.0 REMARK 620 3 ACT C 103 OXT 115.6 110.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 1 N REMARK 620 2 GLU B 16 OE2 102.4 REMARK 620 3 HOH B 220 O 95.7 112.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET C 1 N REMARK 620 2 GLU C 16 OE1 100.8 REMARK 620 3 HOH C 204 O 99.9 99.9 REMARK 620 N 1 2 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 3N30 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CUBIC ZN3-HUB (HUMAN UBIQUITIN) ADDUCT REMARK 900 RELATED ID: 3N32 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN ADDUCT WITH ZEISE'S SALT REMARK 900 RELATED ID: 3EHV RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN UBIQUITIN ZN(II) ADDUCT REMARK 900 RELATED ID: 3EEC RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN UBIQUITIN CD(II) ADDUCT REMARK 900 RELATED ID: 3EFU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN UBIQUITIN-HG(II) ADDUCT REMARK 900 RELATED ID: 4K7U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZN2.3-HUB (HUMAN UBIQUITIN) ADDUCT FROM A REMARK 900 SOLUTION 70 MM ZINC ACETATE/1.3 MM HUB REMARK 900 RELATED ID: 4K7W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZN3-HUB(HUMAN UBIQUITIN) ADDUCT FROM A REMARK 900 SOLUTION 100 MM ZINC ACETATE/1.3 MM HUB DBREF 4K7S A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4K7S B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4K7S C 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY 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 SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 101 1 HET ZN A 102 1 HET EDO A 103 4 HET ZN B 101 1 HET ZN B 102 1 HET ACT B 103 4 HET ZN C 101 1 HET ZN C 102 1 HET ACT C 103 4 HET EDO C 104 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ZN 6(ZN 2+) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 9 ACT 2(C2 H3 O2 1-) FORMUL 14 HOH *352(H2 O) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 GLN A 41 5 5 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 THR B 22 GLY B 35 1 14 HELIX 5 5 PRO B 37 GLN B 41 5 5 HELIX 6 6 LEU B 56 ASN B 60 5 5 HELIX 7 7 THR C 22 GLY C 35 1 14 HELIX 8 8 PRO C 37 ASP C 39 5 3 HELIX 9 9 LEU C 56 ASN C 60 5 5 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 69 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 LEU A 43 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 B 5 THR B 66 VAL B 70 1 O LEU B 69 N LYS B 6 SHEET 4 B 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 C 5 THR C 12 GLU C 16 0 SHEET 2 C 5 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 C 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 C 5 GLN C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 C 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK N MET A 1 ZN ZN A 101 1555 1555 2.29 LINK OE1 GLU A 16 ZN ZN A 101 1555 1555 2.14 LINK OD1 ASP A 21 ZN ZN A 102 1555 1555 2.01 LINK NE2 HIS A 68 ZN ZN B 101 1555 1555 1.99 LINK ZN ZN A 101 O HOH C 223 1555 1555 2.01 LINK ZN ZN A 102 O1 EDO A 103 1555 1555 1.84 LINK ZN ZN A 102 O HOH A 299 1555 1555 1.93 LINK O2 EDO A 103 ZN ZN C 102 1555 1555 2.18 LINK O HOH A 265 ZN ZN B 101 1555 1555 2.60 LINK N MET B 1 ZN ZN B 102 1555 1555 2.03 LINK OE2 GLU B 16 ZN ZN B 102 1555 1555 1.99 LINK NE2 HIS B 68 ZN ZN B 101 1555 1555 2.04 LINK ZN ZN B 101 O HOH B 203 1555 1555 2.13 LINK ZN ZN B 102 O HOH B 220 1555 1555 2.41 LINK N MET C 1 ZN ZN C 101 1555 1555 2.10 LINK OE1 GLU C 16 ZN ZN C 101 1555 1555 1.90 LINK OE1 GLU C 18 ZN ZN C 102 1555 1555 2.08 LINK ZN ZN C 101 O HOH C 204 1555 1555 2.17 LINK ZN ZN C 102 OXT ACT C 103 1555 1555 1.98 SITE 1 AC1 4 MET A 1 GLU A 16 GLU B 51 HOH C 223 SITE 1 AC2 4 ASP A 21 EDO A 103 HOH A 299 GLU B 18 SITE 1 AC3 9 GLU A 18 ASP A 21 ZN A 102 HOH A 300 SITE 2 AC3 9 GLU B 18 ASP B 21 GLU C 18 ZN C 102 SITE 3 AC3 9 ACT C 103 SITE 1 AC4 5 HIS A 68 HOH A 265 LYS B 6 HIS B 68 SITE 2 AC4 5 HOH B 203 SITE 1 AC5 4 MET B 1 GLU B 16 HOH B 220 GLU C 51 SITE 1 AC6 7 ILE B 44 ALA B 46 GLY B 47 HIS B 68 SITE 2 AC6 7 HOH B 266 HOH B 279 HOH B 280 SITE 1 AC7 4 GLU A 51 MET C 1 GLU C 16 HOH C 204 SITE 1 AC8 4 EDO A 103 ASP B 21 GLU C 18 ACT C 103 SITE 1 AC9 6 EDO A 103 GLU B 18 ASP B 21 LYS B 29 SITE 2 AC9 6 GLU C 18 ZN C 102 SITE 1 BC1 4 THR C 7 LEU C 8 LEU C 69 HOH C 322 CRYST1 43.840 50.330 94.030 90.00 90.00 90.00 P 21 21 21 12 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 0.022810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010635 0.00000