10 20 30 40 50 60 70 80 4K7U - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIGASE 17-APR-13 4K7U
TITLE CRYSTAL STRUCTURE OF ZN2.3-HUB (HUMAN UBIQUITIN) ADDUCT FROM A TITLE 2 SOLUTION 70 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 1-76; 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 2 01-MAR-17 4K7U 1 JRNL REVDAT 1 08-MAY-13 4K7U 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,VAGIN,DODSON 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) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20021 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1087 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) : 1461 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.2270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1722 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : 0.06000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.745 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1831 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2462 ; 2.241 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 6.370 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;37.459 ;25.854 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;14.380 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;22.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 293 ; 0.233 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1315 ; 0.011 ; 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): 1113 ; 1.535 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1823 ; 2.618 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 718 ; 4.283 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 629 ; 7.155 ; 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 4K7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-13. REMARK 100 THE RCSB ID CODE IS RCSB079000.
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 : 21184 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : 0.09700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.400 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 (%): 38.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1450, 50MM HEPES PH 7.0, REMARK 280 70 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 21.91000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.19500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.91000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.19500 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 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 NH1 ARG A 72 O HOH A 252 1.68 REMARK 500 OD1 ASP C 32 O HOH C 253 1.82 REMARK 500 O HOH A 256 O HOH A 279 2.06 REMARK 500 OE2 GLU C 51 O HOH C 263 2.09 REMARK 500 ND2 ASN C 60 O HOH C 259 2.11 REMARK 500 OD1 ASP A 39 O2 PEG A 108 2.13 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 NE2 HIS C 68 O2 PEG A 108 1545 1.89 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 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 LEU A 67 CB - CG - CD2 ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP B 39 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 54 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 249 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH B 269 DISTANCE = 5.20 ANGSTROMS REMARK 525 HOH C 278 DISTANCE = 5.82 ANGSTROMS
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 B 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 16 OE2 REMARK 620 2 MET B 1 N 114.2 REMARK 620 N 1 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 GLU A 16 OE1 REMARK 620 2 MET A 1 N 107.4 REMARK 620 3 HOH C 201 O 103.9 99.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 233 O REMARK 620 2 HOH C 254 O 111.5 REMARK 620 3 HOH A 241 O 113.7 117.6 REMARK 620 4 HOH C 271 O 107.0 103.2 102.1 REMARK 620 N 1 2 3 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 GLU C 16 OE1 REMARK 620 2 HOH C 222 O 100.8 REMARK 620 3 MET C 1 N 107.3 100.0 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 HOH C 254 O REMARK 620 2 EDO C 104 O1 117.1 REMARK 620 3 GLU A 18 OE1 97.6 101.3 REMARK 620 4 ASP C 21 OD1 101.9 124.1 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 EDO A 106 O1 REMARK 620 2 HOH A 241 O 114.7 REMARK 620 3 ASP A 21 OD1 121.4 100.8 REMARK 620 N 1 2 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 ACT C 103 O REMARK 620 2 GLU C 18 OE1 108.0 REMARK 620 3 HOH C 233 O 117.7 95.0 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 ACT B 104 OXT REMARK 620 2 HIS B 68 NE2 115.8 REMARK 620 3 HIS A 68 NE2 113.4 105.0 REMARK 620 4 LYS B 6 NZ 115.1 102.6 103.5 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 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 ZN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 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' REMARK 900 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: 4K7S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZN2-HUB (HUMAN UBIQUITIN) ADDUCT FROM REMARK 900 A SOLUTION 35 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 4K7U A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4K7U B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4K7U 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 ZN A 103 1 HET ZN A 104 1 HET ACT A 105 4 HET EDO A 106 4 HET EDO A 107 4 HET PEG A 108 7 HET ZN B 101 1 HET ZN B 102 1 HET ZN B 103 1 HET ACT B 104 4 HET EDO B 105 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 ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER
HETSYN EDO ETHYLENE GLYCOL
FORMUL 4 ZN 9(ZN 2+) FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 9 EDO 4(C2 H6 O2) FORMUL 11 PEG C4 H10 O3 FORMUL 21 HOH *249(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 VAL B 5 O ILE B 13 SHEET 3 B 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 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 69 N LYS C 6 SHEET 4 C 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 C 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45
LINK OE2 GLU B 16 ZN ZN B 102 1555 1555 1.84 LINK OE1 GLU A 16 ZN ZN A 101 1555 1555 1.89 LINK ZN ZN A 104 O HOH C 233 1555 1555 1.89 LINK OE1 GLU C 16 ZN ZN C 101 1555 1555 1.90 LINK ZN ZN A 102 O HOH C 254 1555 1555 1.94 LINK N MET B 1 ZN ZN B 102 1555 1555 1.94 LINK ZN ZN A 103 O1 EDO A 106 1555 1555 1.95 LINK ZN ZN A 102 O1 EDO C 104 1555 1555 1.96 LINK ZN ZN C 102 O ACT C 103 1555 1555 1.96 LINK N MET A 1 ZN ZN A 101 1555 1555 1.97 LINK ZN ZN B 101 OXT ACT B 104 1555 1555 1.98 LINK OE1 GLU A 18 ZN ZN A 102 1555 1555 1.98 LINK ZN ZN A 103 O HOH A 241 1555 1555 1.99 LINK OD1 ASP C 21 ZN ZN A 102 1555 1555 1.99 LINK ZN ZN A 104 O HOH C 254 1555 1555 1.99 LINK OE1 GLU C 18 ZN ZN C 102 1555 1555 1.99 LINK ZN ZN C 102 O HOH C 233 1555 1555 2.02 LINK ZN ZN A 101 O HOH C 201 1555 1555 2.02 LINK NE2 HIS B 68 ZN ZN B 101 1555 1555 2.03 LINK NE2 HIS A 68 ZN ZN B 101 1555 1555 2.03 LINK ZN ZN C 101 O HOH C 222 1555 1555 2.04 LINK OD1 ASP A 21 ZN ZN A 103 1555 1555 2.04 LINK N MET C 1 ZN ZN C 101 1555 1555 2.08 LINK ZN ZN A 104 O HOH A 241 1555 1555 2.15 LINK ZN ZN A 104 O HOH C 271 1555 1555 2.17 LINK NZ LYS B 6 ZN ZN B 101 1555 1555 2.28
SITE 1 AC1 4 MET A 1 GLU A 16 GLU B 51 HOH C 201 SITE 1 AC2 5 GLU A 18 ZN A 104 ASP C 21 EDO C 104 SITE 2 AC2 5 HOH C 254 SITE 1 AC3 5 ASP A 21 ZN A 104 EDO A 106 HOH A 241 SITE 2 AC3 5 GLU B 18 SITE 1 AC4 10 GLU A 18 ZN A 102 ZN A 103 HOH A 241 SITE 2 AC4 10 GLU B 18 GLU C 18 ZN C 102 HOH C 233 SITE 3 AC4 10 HOH C 254 HOH C 271 SITE 1 AC5 3 THR A 14 LYS A 33 HOH B 248 SITE 1 AC6 6 GLU A 16 GLU A 18 ASP A 21 LYS A 29 SITE 2 AC6 6 ZN A 103 GLU B 18 SITE 1 AC7 7 ASP A 58 HOH A 260 HOH A 280 LEU B 15 SITE 2 AC7 7 GLU B 16 LYS B 29 ACT C 103 SITE 1 AC8 7 PRO A 37 ASP A 39 HOH A 283 ALA C 46 SITE 2 AC8 7 HIS C 68 HOH C 217 HOH C 258 SITE 1 AC9 5 HIS A 68 LYS B 6 HIS B 68 ACT B 104 SITE 2 AC9 5 HOH B 256 SITE 1 BC1 5 HOH A 244 MET B 1 GLU B 16 ZN B 103 SITE 2 BC1 5 GLU C 51 SITE 1 BC2 5 ASP A 32 HOH A 244 ZN B 102 GLU C 51 SITE 2 BC2 5 HOH C 242 SITE 1 BC3 8 LYS A 6 THR A 66 HIS A 68 LYS B 6 SITE 2 BC3 8 HIS B 68 ZN B 101 HOH B 256 HOH B 277 SITE 1 BC4 6 LYS A 63 LYS B 48 GLN B 49 GLN C 31 SITE 2 BC4 6 ASP C 32 HOH C 218 SITE 1 BC5 4 GLU A 51 MET C 1 GLU C 16 HOH C 222 SITE 1 BC6 5 ZN A 104 ASP B 21 GLU C 18 ACT C 103 SITE 2 BC6 5 HOH C 233 SITE 1 BC7 9 EDO A 107 GLU B 16 GLU B 18 ASP B 21 SITE 2 BC7 9 LYS B 29 HOH B 265 GLU C 18 ZN C 102 SITE 3 BC7 9 HOH C 271 SITE 1 BC8 7 GLU A 18 ZN A 102 GLU C 18 ASP C 21 SITE 2 BC8 7 LYS C 29 HOH C 270 HOH C 271
CRYST1 43.820 50.390 93.620 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 0.022821 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019845 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010681 0.00000