HEADER LIGASE 04-APR-17 5NLF TITLE CRYSTAL STRUCTURE OF ZN2.7-E16V HUMAN UBIQUITIN (HUB) MUTANT ADDUCT, TITLE 2 FROM A SOLUTION 100 MM ZINC ACETATE/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, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.FALINI REVDAT 4 17-JAN-24 5NLF 1 LINK REVDAT 3 28-MAR-18 5NLF 1 JRNL REVDAT 2 03-JAN-18 5NLF 1 JRNL REMARK REVDAT 1 03-MAY-17 5NLF 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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 30674 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1671 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1705 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : -0.24000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.138 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1791 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1837 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2424 ; 2.433 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4258 ; 1.363 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 6.254 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;36.623 ;26.267 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 366 ;13.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.184 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 296 ; 0.173 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1983 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 347 ; 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): 883 ; 1.810 ; 1.322 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 877 ; 1.759 ; 1.316 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1096 ; 2.547 ; 1.965 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1097 ; 2.546 ; 1.968 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 908 ; 3.386 ; 1.762 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 909 ; 3.384 ; 1.762 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1321 ; 5.179 ; 2.488 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2073 ; 7.111 ;12.244 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1997 ; 6.920 ;11.657 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 5NLF 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_1200004037. 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 : 32385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 FOR SHELL : 6.200 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, REMARK 280 100 MM ZN(CH3COO)2, 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 22.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.26500 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 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 C 215 O HOH C 259 1.80 REMARK 500 OG SER A 20 O HOH A 201 1.84 REMARK 500 O HOH A 203 O HOH A 229 1.87 REMARK 500 OG SER C 20 O HOH C 201 1.92 REMARK 500 NE2 GLN A 40 O HOH A 202 1.98 REMARK 500 NH2 ARG B 54 O HOH B 201 2.05 REMARK 500 CG ASN C 60 O HOH C 204 2.07 REMARK 500 NZ LYS B 11 O HOH B 202 2.14 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 ACT A 110 ZN ZN B 103 2564 1.63 REMARK 500 O HOH A 265 O HOH B 234 3645 2.08 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 ASP B 39 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG B 54 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 54 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 LEU B 67 CB - CG - CD2 ANGL. DEV. = 13.0 DEGREES REMARK 500 ASP C 39 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG C 54 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 54 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU C 67 CB - CG - CD1 ANGL. DEV. = 10.9 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 109 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 GLU B 51 OE2 85.4 REMARK 620 3 ASP C 32 OD1 129.3 144.7 REMARK 620 4 HOH C 208 O 147.6 79.9 66.9 REMARK 620 N 1 2 3 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 18 OE1 REMARK 620 2 ACT A 110 OXT 110.4 REMARK 620 3 ASP C 21 OD1 113.1 117.6 REMARK 620 4 HOH C 224 O 98.3 113.3 102.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 ACT A 110 OXT 88.1 REMARK 620 3 HOH A 241 O 39.4 111.8 REMARK 620 4 HOH C 224 O 42.6 114.0 3.2 REMARK 620 N 1 2 3 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 ACT A 105 OXT 117.2 REMARK 620 3 HOH A 245 O 105.2 116.0 REMARK 620 4 GLU B 18 OE1 46.4 71.4 122.4 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 39 OD2 REMARK 620 2 ACT A 106 OXT 94.1 REMARK 620 3 HIS C 68 NE2 47.6 46.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 107 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 ACT A 108 OXT 117.6 REMARK 620 3 LYS B 6 NZ 103.0 109.2 REMARK 620 4 HIS B 68 NE2 105.5 115.8 104.4 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 HOH A 241 O REMARK 620 2 HOH A 245 O 100.0 REMARK 620 3 HOH B 216 O 103.4 111.8 REMARK 620 4 HOH C 224 O 98.8 121.7 116.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 241 O REMARK 620 2 HOH A 245 O 87.2 REMARK 620 3 GLU B 18 OE1 153.1 81.6 REMARK 620 4 HOH B 216 O 113.0 97.6 92.7 REMARK 620 5 ACT C 101 OXT 86.5 172.2 102.1 89.2 REMARK 620 N 1 2 3 4 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 MET B 1 N REMARK 620 2 HOH B 222 O 75.2 REMARK 620 3 HOH B 242 O 86.1 159.1 REMARK 620 4 HOH B 263 O 145.1 70.0 127.8 REMARK 620 N 1 2 3 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 ASP B 21 OD1 REMARK 620 2 HOH B 216 O 102.3 REMARK 620 3 GLU C 18 OE2 46.3 126.5 REMARK 620 4 ACT C 101 O 118.7 117.0 72.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 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 ACT A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 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, CRYSTALLIZED IN REMARK 900 THE SAME CONDITIONS REMARK 900 RELATED ID: 4K7W RELATED DB: PDB REMARK 900 ZN3-HUB(HUMAN UBIQUITIN) ADDUCT REMARK 900 RELATED ID: 4KTU RELATED DB: PDB REMARK 900 BOVINE TRYPSIN IN COMPLEX WITH MICROVIRIDIN J AT PH 6.5 REMARK 900 RELATED ID: 4KTS RELATED DB: PDB REMARK 900 BOVINE TRYPSIN IN COMPLEX WITH MICROVIRIDIN J AT PH 8.5 DBREF 5NLF A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 5NLF B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 5NLF C 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 5NLF VAL A 16 UNP P0CG48 GLU 16 ENGINEERED MUTATION SEQADV 5NLF VAL B 16 UNP P0CG48 GLU 16 ENGINEERED MUTATION SEQADV 5NLF 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 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 ACT A 106 4 HET ZN A 107 1 HET ACT A 108 4 HET ZN A 109 1 HET ACT A 110 4 HET ZN B 101 1 HET ZN B 102 1 HET ZN B 103 1 HET ZN B 104 1 HET ACT C 101 4 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION FORMUL 4 ZN 10(ZN 2+) FORMUL 8 ACT 5(C2 H3 O2 1-) FORMUL 19 HOH *216(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 ILE A 3 O LEU A 15 SHEET 3 AA1 5 THR A 66 LEU A 69 1 O LEU A 67 N PHE A 4 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 LYS B 6 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 ILE C 3 O LEU C 15 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 N MET A 1 ZN ZN A 109 1555 1555 2.49 LINK OE1 GLU A 18 ZN ZN A 101 1555 1555 1.95 LINK OE1 GLU A 18 ZN ZN B 103 1555 2564 2.67 LINK OD1 ASP A 21 ZN ZN A 102 1555 1555 2.03 LINK OD2 ASP A 39 ZN ZN A 104 1555 1555 1.96 LINK NE2 HIS A 68 ZN ZN A 107 1555 1555 2.02 LINK ZN ZN A 101 OXT ACT A 110 1555 1555 1.93 LINK ZN ZN A 101 OD1 ASP C 21 1555 1555 2.02 LINK ZN ZN A 101 O HOH C 224 1555 1555 1.90 LINK ZN ZN A 102 OXT ACT A 105 1555 1555 1.94 LINK ZN ZN A 102 O HOH A 245 1555 1555 1.93 LINK ZN ZN A 102 OE1 GLU B 18 2565 1555 1.98 LINK ZN ZN A 103 O HOH A 241 1555 1555 2.06 LINK ZN ZN A 103 O HOH A 245 1555 1555 2.00 LINK ZN ZN A 103 O HOH B 216 1555 2564 2.01 LINK ZN ZN A 103 O HOH C 224 1555 1555 2.03 LINK ZN ZN A 104 OXT ACT A 106 1555 1555 2.08 LINK ZN ZN A 104 NE2 HIS C 68 1545 1555 1.98 LINK ZN ZN A 107 OXT ACT A 108 1555 1555 1.99 LINK ZN ZN A 107 NZ LYS B 6 1555 1555 2.01 LINK ZN ZN A 107 NE2 HIS B 68 1555 1555 2.02 LINK ZN ZN A 109 OE2 GLU B 51 3555 1555 2.53 LINK ZN ZN A 109 OD1 ASP C 32 1555 1555 2.65 LINK ZN ZN A 109 O HOH C 208 1555 1555 1.73 LINK OXT ACT A 110 ZN ZN B 103 1555 2564 1.84 LINK O HOH A 241 ZN ZN B 103 2565 1555 2.11 LINK O HOH A 241 ZN ZN B 104 2565 1555 1.97 LINK O HOH A 245 ZN ZN B 104 2565 1555 2.51 LINK N MET B 1 ZN ZN B 101 1555 1555 2.04 LINK OE1 GLU B 18 ZN ZN B 104 1555 1555 1.89 LINK OD1 ASP B 21 ZN ZN B 102 1555 1555 2.01 LINK ZN ZN B 101 O HOH B 222 1555 1555 2.61 LINK ZN ZN B 101 O HOH B 242 1555 1555 2.19 LINK ZN ZN B 101 O HOH B 263 1555 1555 1.94 LINK ZN ZN B 102 O HOH B 216 1555 1555 1.98 LINK ZN ZN B 102 OE2 GLU C 18 2564 1555 2.00 LINK ZN ZN B 102 O ACT C 101 1555 2565 1.96 LINK ZN ZN B 103 O HOH C 224 1555 2565 2.44 LINK ZN ZN B 104 O HOH B 216 1555 1555 1.87 LINK ZN ZN B 104 OXT ACT C 101 1555 2565 2.39 SITE 1 AC1 6 GLU A 18 ZN A 103 ACT A 110 ZN B 103 SITE 2 AC1 6 ASP C 21 HOH C 224 SITE 1 AC2 6 ASP A 21 ZN A 103 ACT A 105 HOH A 245 SITE 2 AC2 6 GLU B 18 ZN B 104 SITE 1 AC3 12 GLU A 18 ZN A 101 ZN A 102 HOH A 241 SITE 2 AC3 12 HOH A 245 GLU B 18 ZN B 102 ZN B 103 SITE 3 AC3 12 ZN B 104 HOH B 216 GLU C 18 HOH C 224 SITE 1 AC4 3 ASP A 39 ACT A 106 HIS C 68 SITE 1 AC5 10 VAL A 16 GLU A 18 ASP A 21 LYS A 29 SITE 2 AC5 10 ZN A 102 HOH A 228 HOH A 241 GLU B 18 SITE 3 AC5 10 ZN B 103 ZN B 104 SITE 1 AC6 5 PRO A 37 ASP A 39 ZN A 104 HOH A 244 SITE 2 AC6 5 HIS C 68 SITE 1 AC7 4 HIS A 68 ACT A 108 LYS B 6 HIS B 68 SITE 1 AC8 6 LYS A 6 THR A 66 HIS A 68 ZN A 107 SITE 2 AC8 6 LYS B 6 HIS B 68 SITE 1 AC9 5 MET A 1 HOH A 212 GLU B 51 ASP C 32 SITE 2 AC9 5 HOH C 208 SITE 1 AD1 9 GLU A 18 ZN A 101 HOH A 223 HOH A 241 SITE 2 AD1 9 ZN B 103 VAL C 16 GLU C 18 ASP C 21 SITE 3 AD1 9 LYS C 29 SITE 1 AD2 4 MET B 1 HOH B 222 HOH B 242 HOH B 263 SITE 1 AD3 6 ZN A 103 ASP B 21 ZN B 104 HOH B 216 SITE 2 AD3 6 GLU C 18 ACT C 101 SITE 1 AD4 7 GLU A 18 ZN A 101 ZN A 103 ACT A 105 SITE 2 AD4 7 ACT A 110 HOH A 241 HOH C 224 SITE 1 AD5 9 ZN A 102 ZN A 103 ACT A 105 HOH A 241 SITE 2 AD5 9 HOH A 245 GLU B 18 ZN B 102 HOH B 216 SITE 3 AD5 9 ACT C 101 SITE 1 AD6 10 HOH A 241 VAL B 16 GLU B 18 ASP B 21 SITE 2 AD6 10 LYS B 29 ZN B 102 ZN B 104 HOH B 216 SITE 3 AD6 10 GLU C 18 HOH C 222 CRYST1 44.410 50.530 93.680 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 0.022517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010675 0.00000