HEADER LIGASE 04-APR-17 5NLJ TITLE CRYSTAL STRUCTURE OF ZN3-E16V HUMAN UBIQUITIN (HUB) MUTANT ADDUCT, TITLE 2 FROM A SOLUTION 70 MM ZINC ACETATE/20% V/V TFE/1.3 MM E16V HUB COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E16V MUTANT, LIGASE, UBIQUITINATION, PROTEASOME DEGRADATION, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.FALINI REVDAT 6 17-JAN-24 5NLJ 1 LINK REVDAT 5 28-MAR-18 5NLJ 1 JRNL REVDAT 4 31-JAN-18 5NLJ 1 AUTHOR REVDAT 3 03-JAN-18 5NLJ 1 JRNL REVDAT 2 06-DEC-17 5NLJ 1 REMARK REVDAT 1 26-APR-17 5NLJ 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 28506 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1521 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) : 1340 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1694 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : 0.74000 REMARK 3 B33 (A**2) : -0.28000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.365 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1775 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2393 ; 2.384 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 6.079 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;33.361 ;26.216 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;13.182 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;26.237 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 291 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1276 ; 0.013 ; 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): 869 ; 1.760 ; 1.440 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1076 ; 2.440 ; 2.142 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 906 ; 3.466 ; 1.860 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2768 ; 6.668 ;14.041 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 : NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5NLJ 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_1200004169. 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 27.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11300 REMARK 200 FOR THE DATA SET : 11.0000 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 (%) : 68.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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, 70 REMARK 280 MM ZN(CH3COO)2 AND 20% 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 22.18000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.70500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.70500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.98500 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 ARG B 72 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 NZ LYS B 6 ZN ZN A 107 1.52 REMARK 500 O HOH B 201 O HOH B 248 2.08 REMARK 500 OD2 ASP B 52 O HOH B 201 2.08 REMARK 500 O2 PEG B 102 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 B 245 O HOH C 206 2565 1.98 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 LEU A 67 CB - CG - CD1 ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -4.3 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 B 289 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH B 290 DISTANCE = 7.25 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 A 109 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 GLU B 51 OE2 88.1 REMARK 620 3 ASP C 32 OD1 123.2 146.8 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 GLU A 18 OE1 REMARK 620 2 ACT A 108 OXT 110.5 REMARK 620 3 ASP C 21 OD1 110.9 119.7 REMARK 620 4 HOH C 222 O 99.1 116.1 98.1 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 ASP A 21 OD1 REMARK 620 2 ACT A 102 O 117.5 REMARK 620 3 HOH A 213 O 101.4 119.5 REMARK 620 4 GLU B 18 OE1 47.7 70.6 120.1 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 103 OXT 97.4 REMARK 620 3 HIS C 68 NE2 47.2 50.2 REMARK 620 4 ACT C 101 O 105.1 104.5 114.2 REMARK 620 N 1 2 3 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 101 OXT 112.2 REMARK 620 3 HIS B 68 NE2 102.4 112.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 205 O REMARK 620 2 HOH A 213 O 108.8 REMARK 620 3 HOH B 216 O 105.2 112.5 REMARK 620 4 HOH C 222 O 102.5 116.0 110.7 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 MET B 1 N REMARK 620 2 HOH B 278 O 134.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 11 NZ REMARK 620 2 GLU B 34 OE1 112.9 REMARK 620 3 GLU B 34 OE2 80.9 56.0 REMARK 620 4 HOH B 269 O 132.0 102.9 94.5 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 ASP B 21 OD1 REMARK 620 2 ACT B 101 O 121.0 REMARK 620 3 HOH B 216 O 101.1 120.1 REMARK 620 4 GLU C 18 OE1 47.6 73.4 128.0 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 ACT 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 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 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ETF B 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K7S RELATED DB: PDB REMARK 900 WILD-TYPE PROTEIN REMARK 900 RELATED ID: 4K7U RELATED DB: PDB REMARK 900 RELATED ID: 4K7W RELATED DB: PDB REMARK 900 RELATED ID: 3EHV RELATED DB: PDB DBREF 5NLJ A 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5NLJ B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5NLJ C 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5NLJ VAL A 16 UNP P0CG47 GLU 16 ENGINEERED MUTATION SEQADV 5NLJ VAL B 16 UNP P0CG47 GLU 16 ENGINEERED MUTATION SEQADV 5NLJ VAL C 16 UNP P0CG47 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 ACT A 103 4 HET ZN A 104 1 HET ZN A 105 1 HET ZN A 106 1 HET ZN A 107 1 HET ACT A 108 4 HET ZN A 109 1 HET ACT B 101 4 HET PEG B 102 7 HET ZN B 103 1 HET ZN B 104 1 HET ZN B 105 1 HET ZN B 106 1 HET ETF B 107 6 HET ACT C 101 4 HET EDO C 102 4 HETNAM ACT ACETATE ION HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ETF TRIFLUOROETHANOL HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ACT 6(C2 H3 O2 1-) FORMUL 7 ZN 9(ZN 2+) FORMUL 14 PEG C4 H10 O3 FORMUL 19 ETF C2 H3 F3 O FORMUL 21 EDO C2 H6 O2 FORMUL 22 HOH *252(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 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 67 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 2.36 LINK OE1 GLU A 18 ZN ZN A 104 1555 1555 1.99 LINK OD1 ASP A 21 ZN ZN A 105 1555 1555 2.01 LINK OD2 ASP A 39 ZN ZN A 106 1555 1555 2.02 LINK NE2 HIS A 68 ZN ZN A 107 1555 1555 2.07 LINK OXT ACT A 101 ZN ZN A 107 1555 1555 2.15 LINK O ACT A 102 ZN ZN A 105 1555 1555 1.92 LINK OXT ACT A 103 ZN ZN A 106 1555 1555 1.85 LINK ZN ZN A 104 OXT ACT A 108 1555 1555 1.95 LINK ZN ZN A 104 OD1 ASP C 21 1555 1555 2.04 LINK ZN ZN A 104 O HOH C 222 1555 1555 1.94 LINK ZN ZN A 105 O HOH A 213 1555 1555 1.90 LINK ZN ZN A 105 OE1 GLU B 18 2565 1555 2.03 LINK ZN ZN A 106 NE2 HIS C 68 1545 1555 1.91 LINK ZN ZN A 106 O ACT C 101 1555 1565 1.89 LINK ZN ZN A 107 NE2 HIS B 68 1555 1555 1.99 LINK ZN ZN A 109 OE2 GLU B 51 3555 1555 2.32 LINK ZN ZN A 109 OD1 ASP C 32 1555 1555 2.49 LINK O HOH A 205 ZN ZN B 105 2565 1555 1.97 LINK O HOH A 213 ZN ZN B 105 2565 1555 2.14 LINK N MET B 1 ZN ZN B 103 1555 1555 2.05 LINK NZ LYS B 11 ZN ZN B 106 1555 1555 1.98 LINK OD1 ASP B 21 ZN ZN B 104 1555 1555 1.95 LINK OE1 GLU B 34 ZN ZN B 106 1555 1555 2.20 LINK OE2 GLU B 34 ZN ZN B 106 1555 1555 2.47 LINK O ACT B 101 ZN ZN B 104 1555 1555 1.97 LINK ZN ZN B 103 O HOH B 278 1555 1555 2.12 LINK ZN ZN B 104 O HOH B 216 1555 1555 1.98 LINK ZN ZN B 104 OE1 GLU C 18 2564 1555 2.00 LINK ZN ZN B 105 O HOH B 216 1555 1555 2.07 LINK ZN ZN B 105 O HOH C 222 1555 2565 2.21 LINK ZN ZN B 106 O HOH B 269 1555 1555 2.39 SITE 1 AC1 6 LYS A 6 THR A 66 HIS A 68 ZN A 107 SITE 2 AC1 6 LYS B 6 HIS B 68 SITE 1 AC2 6 VAL A 16 GLU A 18 ASP A 21 LYS A 29 SITE 2 AC2 6 ZN A 105 GLU B 18 SITE 1 AC3 5 ASP A 39 ZN A 106 HOH A 245 HIS C 68 SITE 2 AC3 5 ACT C 101 SITE 1 AC4 5 GLU A 18 ACT A 108 ZN B 105 ASP C 21 SITE 2 AC4 5 HOH C 222 SITE 1 AC5 6 ASP A 21 ACT A 102 HOH A 213 GLU B 18 SITE 2 AC5 6 PEG B 102 ZN B 105 SITE 1 AC6 4 ASP A 39 ACT A 103 HIS C 68 ACT C 101 SITE 1 AC7 4 HIS A 68 ACT A 101 LYS B 6 HIS B 68 SITE 1 AC8 9 GLU A 18 ZN A 104 HOH A 205 HOH A 224 SITE 2 AC8 9 ZN B 105 VAL C 16 GLU C 18 ASP C 21 SITE 3 AC8 9 LYS C 29 SITE 1 AC9 3 MET A 1 GLU B 51 ASP C 32 SITE 1 AD1 9 HOH A 205 VAL B 16 GLU B 18 ASP B 21 SITE 2 AD1 9 LYS B 29 ZN B 104 HOH B 215 HOH B 216 SITE 3 AD1 9 GLU C 18 SITE 1 AD2 13 SER A 20 ASP A 21 ASN A 25 ZN A 105 SITE 2 AD2 13 HOH A 213 SER B 20 ASN B 25 ZN B 105 SITE 3 AD2 13 HOH B 202 SER C 20 ASP C 21 ASN C 25 SITE 4 AD2 13 HOH C 222 SITE 1 AD3 3 MET B 1 HOH B 228 HOH B 278 SITE 1 AD4 5 ASP B 21 ACT B 101 ZN B 105 HOH B 216 SITE 2 AD4 5 GLU C 18 SITE 1 AD5 12 GLU A 18 ZN A 104 ZN A 105 ACT A 108 SITE 2 AD5 12 HOH A 205 HOH A 213 GLU B 18 PEG B 102 SITE 3 AD5 12 ZN B 104 HOH B 216 GLU C 18 HOH C 222 SITE 1 AD6 4 LYS B 11 GLU B 34 HOH B 258 HOH B 269 SITE 1 AD7 5 LEU B 8 ILE B 36 GLN B 40 HOH B 250 SITE 2 AD7 5 HOH C 248 SITE 1 AD8 6 ASP A 39 ACT A 103 ZN A 106 ALA C 46 SITE 2 AD8 6 HIS C 68 HOH C 230 SITE 1 AD9 4 SER B 20 THR B 55 HOH C 206 HOH C 209 CRYST1 44.360 49.970 93.410 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 0.022543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010705 0.00000