HEADER LIGASE 04-APR-17 5NLI TITLE CRYSTAL STRUCTURE OF ZN2-E16V HUMAN UBIQUITIN (HUB) MUTANT ADDUCT, TITLE 2 FROM A SOLUTION 35 MM ZINC ACETATE/10% V/V TFE/1.3 MM E16V HUB COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-C; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES; COMPND 5 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E16V MUTANT, LIGASE, UBIQUITINATION, PROTEASOME DEGRADATION EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.FALINI REVDAT 4 17-JAN-24 5NLI 1 LINK REVDAT 3 28-MAR-18 5NLI 1 JRNL REVDAT 2 03-JAN-18 5NLI 1 JRNL REMARK REVDAT 1 03-MAY-17 5NLI 0 JRNL AUTH S.FERMANI,M.CALVARESI,V.MANGINI,G.FALINI,A.BOTTONI,G.NATILE, JRNL AUTH 2 F.ARNESANO JRNL TITL AGGREGATION PATHWAYS OF NATIVE-LIKE UBIQUITIN PROMOTED BY JRNL TITL 2 SINGLE-POINT MUTATION, METAL ION CONCENTRATION, AND JRNL TITL 3 DIELECTRIC CONSTANT OF THE MEDIUM. JRNL REF CHEMISTRY V. 24 4140 2018 JRNL REFN ISSN 1521-3765 JRNL PMID 29266436 JRNL DOI 10.1002/CHEM.201705543 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.FERMANI,G.FALINI,M.CALVARESI,A.BOTTONI,V.CALO,V.MANGINI, REMARK 1 AUTH 2 F.ARNESANO,G.NATILE REMARK 1 TITL CONFORMATIONAL SELECTION OF UBIQUITIN QUATERNARY STRUCTURES REMARK 1 TITL 2 DRIVEN BY ZINC IONS. REMARK 1 REF CHEMISTRY V. 19 15480 2013 REMARK 1 REFN ISSN 1521-3765 REMARK 1 PMID 24123543 REMARK 1 DOI 10.1002/CHEM.201302229 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 29709 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1480 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -0.32000 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): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.202 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1844 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1903 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2486 ; 2.258 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4392 ; 1.094 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 5.968 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;33.893 ;25.309 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 377 ;13.279 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 300 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2026 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 373 ; 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): 896 ; 1.789 ; 1.486 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 890 ; 1.758 ; 1.478 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1112 ; 2.633 ; 2.203 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1113 ; 2.633 ; 2.207 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 948 ; 3.229 ; 1.966 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 948 ; 3.221 ; 1.965 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1368 ; 4.913 ; 2.783 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2134 ; 7.242 ;13.560 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2134 ; 7.243 ;13.546 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 : 1.20 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 REMARK 4 REMARK 4 5NLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.0 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) : 1.265 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31309 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 27.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29300 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3EHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-30% (W/V) PEG 1450, 50 MM HEPES, 35 REMARK 280 MM ZN(CH3COO)2 AND 10% V/V TFE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 22.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.88000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.88000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.36500 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 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 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 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 GLY A 75 REMARK 465 GLY A 76 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 LEU A 71 O HOH A 201 1.92 REMARK 500 F2 ETF B 104 O HOH B 208 1.97 REMARK 500 N MET B 1 O HOH B 201 2.11 REMARK 500 NH2 ARG B 54 O HOH B 202 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 O HOH A 260 O HOH B 245 3645 2.16 REMARK 500 O HOH B 201 O HOH C 263 3655 2.19 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 SER C 20 CB SER C 20 OG 0.081 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 B 42 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 54 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 SER C 20 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG C 54 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES 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 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 ACT A 109 OXT 112.7 REMARK 620 3 ASP C 21 OD1 110.4 119.2 REMARK 620 4 HOH C 228 O 96.5 114.7 100.4 REMARK 620 N 1 2 3 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 ASP A 21 OD1 REMARK 620 2 ACT A 101 OXT 116.2 REMARK 620 3 HOH A 232 O 104.5 120.8 REMARK 620 4 GLU B 18 OE1 45.8 71.5 122.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD2 REMARK 620 2 ACT A 102 O 97.1 REMARK 620 3 HOH A 251 O 99.9 94.6 REMARK 620 4 HIS C 68 NE2 47.2 50.5 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 108 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 ACT A 107 OXT 116.8 REMARK 620 3 LYS B 6 NZ 103.9 103.1 REMARK 620 4 HIS B 68 NE2 104.4 120.2 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 232 O REMARK 620 2 HOH A 240 O 101.5 REMARK 620 3 HOH B 218 O 112.0 103.6 REMARK 620 4 HOH C 228 O 117.2 103.6 116.2 REMARK 620 N 1 2 3 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 ASP B 21 OD1 REMARK 620 2 HOH B 218 O 104.0 REMARK 620 3 GLU C 18 OE2 44.9 126.0 REMARK 620 4 ACT C 101 O 119.8 115.1 75.0 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 ACT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT 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 ZN A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ETF B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EHV RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN ZN(II) ADDUCT WILD-TYPE PROTEIN REMARK 900 RELATED ID: 4KTS RELATED DB: PDB REMARK 900 BOVINE TRYPSIN IN COMPLEX WITH MICROVIRIDIN J AT PH 8.5 REMARK 900 RELATED ID: 4K7U RELATED DB: PDB REMARK 900 ZN2.3-HUB (HUMAN UBIQUITIN) ADDUCT REMARK 900 RELATED ID: 4KTW RELATED DB: PDB REMARK 900 LACTOCOCCUS PHAGE 67 RUVC - APO FORM DBREF 5NLI A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 5NLI B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 5NLI C 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 5NLI VAL A 16 UNP P0CG48 GLU 16 ENGINEERED MUTATION SEQADV 5NLI VAL B 16 UNP P0CG48 GLU 16 ENGINEERED MUTATION SEQADV 5NLI VAL C 16 UNP P0CG48 GLU 16 ENGINEERED MUTATION SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU VAL 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 VAL 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 VAL 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 ACT A 101 4 HET ACT A 102 4 HET ZN A 103 1 HET ZN A 104 1 HET ZN A 105 1 HET ZN A 106 1 HET ACT A 107 4 HET ZN A 108 1 HET ACT A 109 4 HET ZN B 101 1 HET EDO B 102 4 HET EDO B 103 4 HET ETF B 104 6 HET ACT C 101 4 HETNAM ACT ACETATE ION HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ETF TRIFLUOROETHANOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ACT 5(C2 H3 O2 1-) FORMUL 6 ZN 6(ZN 2+) FORMUL 14 EDO 2(C2 H6 O2) FORMUL 16 ETF C2 H3 F3 O FORMUL 18 HOH *234(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 GLN A 41 5 5 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 THR B 22 GLY B 35 1 14 HELIX 5 AA5 PRO B 37 GLN B 41 5 5 HELIX 6 AA6 LEU B 56 ASN B 60 5 5 HELIX 7 AA7 THR C 22 GLY C 35 1 14 HELIX 8 AA8 PRO C 37 ASP C 39 5 3 HELIX 9 AA9 LEU C 56 ASN C 60 5 5 SHEET 1 AA1 5 THR A 12 VAL A 16 0 SHEET 2 AA1 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 69 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 LEU A 43 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 5 THR B 12 VAL B 16 0 SHEET 2 AA2 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 AA2 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 AA2 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA3 5 THR C 12 VAL C 16 0 SHEET 2 AA3 5 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 AA3 5 THR C 66 LEU C 71 1 O LEU C 69 N LYS C 6 SHEET 4 AA3 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA3 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK OE1 GLU A 18 ZN ZN A 103 1555 1555 1.97 LINK OD1 ASP A 21 ZN ZN A 104 1555 1555 2.08 LINK OD2 ASP A 39 ZN ZN A 106 1555 1555 2.03 LINK NE2 HIS A 68 ZN ZN A 108 1555 1555 2.08 LINK OXT ACT A 101 ZN ZN A 104 1555 1555 1.93 LINK O ACT A 102 ZN ZN A 106 1555 1555 1.76 LINK ZN ZN A 103 OXT ACT A 109 1555 1555 1.96 LINK ZN ZN A 103 OD1 ASP C 21 1555 1555 1.98 LINK ZN ZN A 103 O HOH C 228 1555 1555 1.90 LINK ZN ZN A 104 O HOH A 232 1555 1555 1.97 LINK ZN ZN A 104 OE1 GLU B 18 2565 1555 1.97 LINK ZN ZN A 105 O HOH A 232 1555 1555 1.96 LINK ZN ZN A 105 O HOH A 240 1555 1555 2.06 LINK ZN ZN A 105 O HOH B 218 1555 2564 2.03 LINK ZN ZN A 105 O HOH C 228 1555 1555 2.12 LINK ZN ZN A 106 O HOH A 251 1555 1555 2.13 LINK ZN ZN A 106 NE2 HIS C 68 1545 1555 1.92 LINK OXT ACT A 107 ZN ZN A 108 1555 1555 1.97 LINK ZN ZN A 108 NZ LYS B 6 1555 1555 2.39 LINK ZN ZN A 108 NE2 HIS B 68 1555 1555 2.06 LINK OD1 ASP B 21 ZN ZN B 101 1555 1555 2.00 LINK ZN ZN B 101 O HOH B 218 1555 1555 2.00 LINK ZN ZN B 101 OE2 GLU C 18 2564 1555 1.99 LINK ZN ZN B 101 O ACT C 101 1555 2565 2.00 SITE 1 AC1 8 VAL A 16 GLU A 18 ASP A 21 LYS A 29 SITE 2 AC1 8 ZN A 104 HOH A 240 HOH A 243 GLU B 18 SITE 1 AC2 5 PRO A 37 ASP A 39 ZN A 106 HOH A 251 SITE 2 AC2 5 HIS C 68 SITE 1 AC3 5 GLU A 18 ZN A 105 ACT A 109 ASP C 21 SITE 2 AC3 5 HOH C 228 SITE 1 AC4 5 ASP A 21 ACT A 101 ZN A 105 HOH A 232 SITE 2 AC4 5 GLU B 18 SITE 1 AC5 10 GLU A 18 ZN A 103 ZN A 104 HOH A 232 SITE 2 AC5 10 HOH A 240 GLU B 18 ZN B 101 HOH B 218 SITE 3 AC5 10 GLU C 18 HOH C 228 SITE 1 AC6 5 ASP A 39 ACT A 102 HOH A 251 HIS C 68 SITE 2 AC6 5 HOH C 258 SITE 1 AC7 6 LYS A 6 THR A 66 HIS A 68 ZN A 108 SITE 2 AC7 6 LYS B 6 HIS B 68 SITE 1 AC8 4 HIS A 68 ACT A 107 LYS B 6 HIS B 68 SITE 1 AC9 8 GLU A 18 ZN A 103 HOH A 225 HOH A 240 SITE 2 AC9 8 VAL C 16 GLU C 18 ASP C 21 LYS C 29 SITE 1 AD1 5 ZN A 105 ASP B 21 HOH B 218 GLU C 18 SITE 2 AD1 5 ACT C 101 SITE 1 AD2 6 LYS A 48 ASN A 60 LYS B 11 LYS B 33 SITE 2 AD2 6 GLU B 34 HOH B 225 SITE 1 AD3 5 LYS B 48 ASN B 60 HOH B 209 LYS C 33 SITE 2 AD3 5 GLU C 34 SITE 1 AD4 8 GLN A 2 THR A 14 ASP B 52 ARG B 72 SITE 2 AD4 8 HOH B 205 HOH B 208 HOH B 219 HOH B 228 SITE 1 AD5 9 HOH A 240 VAL B 16 GLU B 18 ASP B 21 SITE 2 AD5 9 LYS B 29 ZN B 101 HOH B 218 GLU C 18 SITE 3 AD5 9 HOH C 232 CRYST1 44.450 50.730 93.760 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 0.022497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010666 0.00000