HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-OCT-04 1XTM TITLE CRYSTAL STRUCTURE OF THE DOUBLE MUTANT Y88H-P104H OF A SOD-LIKE TITLE 2 PROTEIN FROM BACILLUS SUBTILIS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL SUPEROXIDE DISMUTASE-LIKE PROTEIN YOJM; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TOP1 KEYWDS SOD, CU-ZN SOD, SOD-LIKE, SUPEROXIDE DISMUTASE MUTANTS, STRUCTURAL KEYWDS 2 GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR V.CALDERONE,S.MANGANI,L.BANCI,M.BENVENUTI,I.BERTINI,A.FANTONI, AUTHOR 2 M.S.VIEZZOLI REVDAT 5 25-OCT-23 1XTM 1 REMARK REVDAT 4 10-NOV-21 1XTM 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1XTM 1 VERSN REVDAT 2 24-FEB-09 1XTM 1 VERSN REVDAT 1 04-OCT-05 1XTM 0 JRNL AUTH L.BANCI,M.BENVENUTI,I.BERTINI,D.E.CABELLI,V.CALDERONE, JRNL AUTH 2 A.FANTONI,S.MANGANI,M.MIGLIARDI,M.S.VIEZZOLI JRNL TITL FROM AN INACTIVE PROKARYOTIC SOD HOMOLOGUE TO AN ACTIVE JRNL TITL 2 PROTEIN THROUGH SITE-DIRECTED MUTAGENESIS. JRNL REF J.AM.CHEM.SOC. V. 127 13287 2005 JRNL REFN ISSN 0002-7863 JRNL PMID 16173759 JRNL DOI 10.1021/JA052790O REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.BANCI,I.BERTINI,V.CALDERONE,F.CRAMARO,R.DEL CONTE, REMARK 1 AUTH 2 A.FANTONI,S.MANGANI,A.QUATTRONE,M.S.VIEZZOLI REMARK 1 TITL A PROKARYOTIC SUPEROXIDE DISMUTASE PARALOG LACKING TWO CU REMARK 1 TITL 2 LIGANDS: FROM LARGELY UNSTRUCTURED IN SOLUTION TO ORDERED IN REMARK 1 TITL 3 THE CRYSTAL. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 102 7541 2005 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 15897454 REMARK 1 DOI 10.1073/PNAS.0502450102 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39853 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 3320 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2927 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.4740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36000 REMARK 3 B22 (A**2) : 2.06000 REMARK 3 B33 (A**2) : -0.70000 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): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.430 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2324 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3138 ; 1.802 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ;17.208 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;41.982 ;25.439 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 369 ;18.564 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.000 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 331 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1822 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1081 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1502 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.235 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.121 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 60 ; 0.253 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.144 ; 0.200 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): 1544 ; 1.183 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2372 ; 1.662 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 850 ; 2.346 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 766 ; 3.512 ; 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): 7 ;22.781 ; 3.000 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: NULL REMARK 4 REMARK 4 1XTM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030754. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27680 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL FOCUSSING MONO REMARK 200 CHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL FOCUSSING MONO REMARK 200 CHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : 0.47800 REMARK 200 FOR SHELL : 1.600 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: 1S4I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE, 30% PEG4000, 0.2M REMARK 280 AMMONIUM SULPHATE, 1MM ZNCL2, PH 4.6, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.23100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.23100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.17500 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 300 REMARK: THE PROTEIN IS A MONOMER IN VIVO BUT THERE ARE TWO REMARK 300 MOLECULES. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -125.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 26.23100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -52.17500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 117.51200 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 LYS B 22 REMARK 465 PRO B 23 REMARK 465 PRO B 24 REMARK 465 ASP B 25 REMARK 465 PRO B 26 REMARK 465 PRO B 27 REMARK 465 ASN B 28 REMARK 465 ARG B 29 REMARK 465 VAL B 30 REMARK 465 PRO B 31 REMARK 465 GLU B 32 REMARK 465 LYS B 33 REMARK 465 LYS B 34 REMARK 465 VAL B 35 REMARK 465 VAL B 36 REMARK 465 GLU B 37 REMARK 465 THR B 38 REMARK 465 ASN B 192 REMARK 465 ASN B 193 REMARK 465 GLU B 194 REMARK 465 LYS B 195 REMARK 465 GLN B 196 REMARK 465 LYS A 22 REMARK 465 PRO A 23 REMARK 465 PRO A 24 REMARK 465 ASP A 25 REMARK 465 PRO A 26 REMARK 465 PRO A 27 REMARK 465 ASN A 28 REMARK 465 ARG A 29 REMARK 465 VAL A 30 REMARK 465 PRO A 31 REMARK 465 GLU A 32 REMARK 465 LYS A 33 REMARK 465 LYS A 34 REMARK 465 VAL A 35 REMARK 465 VAL A 36 REMARK 465 GLU A 37 REMARK 465 THR A 38 REMARK 465 SER A 39 REMARK 465 ASN A 192 REMARK 465 ASN A 193 REMARK 465 GLU A 194 REMARK 465 LYS A 195 REMARK 465 GLN A 196 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 GLY A 119 N HIS A 120 1.57 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 ASP B 144 C THR B 145 N 0.165 REMARK 500 GLY A 119 C HIS A 120 N -0.578 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 ALA B 101 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 GLY B 102 N - CA - C ANGL. DEV. = -22.2 DEGREES REMARK 500 GLY B 103 N - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP B 157 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 65 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLY A 119 CA - C - N ANGL. DEV. = 19.4 DEGREES REMARK 500 GLY A 119 O - C - N ANGL. DEV. = -18.9 DEGREES REMARK 500 HIS A 120 C - N - CA ANGL. DEV. = 26.0 DEGREES REMARK 500 HIS A 120 CA - C - O ANGL. DEV. = 19.7 DEGREES REMARK 500 ASP A 124 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 LEU A 190 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA B 40 -18.83 93.30 REMARK 500 ASN B 106 58.39 -145.42 REMARK 500 LEU B 156 49.11 -97.47 REMARK 500 LEU B 173 -45.75 -148.01 REMARK 500 PHE A 85 115.20 -160.36 REMARK 500 SER A 100 72.15 -107.94 REMARK 500 ALA A 101 -147.65 -116.21 REMARK 500 ASN A 106 57.79 -141.48 REMARK 500 ASP A 133 -62.05 14.40 REMARK 500 LEU A 173 -52.99 -143.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 101 GLY B 102 147.36 REMARK 500 GLY B 102 GLY B 103 -134.04 REMARK 500 LEU B 190 GLY B 191 138.31 REMARK 500 GLY A 119 HIS A 120 -90.64 REMARK 500 ALA A 132 ASP A 133 141.59 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 B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 71 NE2 REMARK 620 2 ASP B 137 OD1 108.3 REMARK 620 3 HIS A 71 NE2 104.8 99.1 REMARK 620 4 ASP A 137 OD1 97.9 134.0 110.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 500 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 86 ND1 REMARK 620 2 HIS B 88 NE2 126.7 REMARK 620 3 HIS B 166 NE2 101.0 127.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 89 O REMARK 620 2 ASP B 157 OD2 153.3 REMARK 620 3 ASP B 157 OD1 152.7 53.9 REMARK 620 4 GLY B 160 O 71.5 135.1 81.3 REMARK 620 5 HOH B 628 O 84.4 95.5 94.1 84.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 104 ND1 REMARK 620 2 HIS B 112 ND1 111.8 REMARK 620 3 HIS B 121 ND1 104.4 120.2 REMARK 620 4 ASP B 124 OD2 107.9 100.7 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 ASP B 144 OD2 136.1 REMARK 620 3 HOH B 553 O 81.0 123.3 REMARK 620 4 HOH B 642 O 108.1 80.2 136.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 503 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 ND1 REMARK 620 2 HIS A 88 NE2 130.9 REMARK 620 3 HIS A 104 NE2 93.5 95.5 REMARK 620 4 HIS A 166 NE2 91.1 115.6 133.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 ND1 REMARK 620 2 HIS A 112 ND1 112.7 REMARK 620 3 HIS A 121 ND1 106.7 123.5 REMARK 620 4 ASP A 124 OD2 107.2 90.0 115.2 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 CU B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S4I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SOD-LIKE PROTEIN FROM BACILLUS SUBTILIS REMARK 900 CRYSTALLISED IN THE PRESENCE OF ZINC REMARK 900 RELATED ID: 1XTL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P104H MUTANT OF SOD-LIKE PROTEIN DBREF 1XTM B 22 196 UNP O31851 YOJM_BACSU 22 196 DBREF 1XTM A 22 196 UNP O31851 YOJM_BACSU 22 196 SEQADV 1XTM HIS B 88 UNP O31851 TYR 88 ENGINEERED MUTATION SEQADV 1XTM HIS B 104 UNP O31851 PRO 104 ENGINEERED MUTATION SEQADV 1XTM HIS A 88 UNP O31851 TYR 88 ENGINEERED MUTATION SEQADV 1XTM HIS A 104 UNP O31851 PRO 104 ENGINEERED MUTATION SEQRES 1 B 175 LYS PRO PRO ASP PRO PRO ASN ARG VAL PRO GLU LYS LYS SEQRES 2 B 175 VAL VAL GLU THR SER ALA PHE GLY HIS HIS VAL GLN LEU SEQRES 3 B 175 VAL ASN ARG GLU GLY LYS ALA VAL GLY PHE ILE GLU ILE SEQRES 4 B 175 LYS GLU SER ASP ASP GLU GLY LEU ASP ILE HIS ILE SER SEQRES 5 B 175 ALA ASN SER LEU ARG PRO GLY ALA SER LEU GLY PHE HIS SEQRES 6 B 175 ILE HIS GLU LYS GLY SER CYS VAL ARG PRO ASP PHE GLU SEQRES 7 B 175 SER ALA GLY GLY HIS PHE ASN PRO LEU ASN LYS GLU HIS SEQRES 8 B 175 GLY PHE ASN ASN PRO MET GLY HIS HIS ALA GLY ASP LEU SEQRES 9 B 175 PRO ASN LEU GLU VAL GLY ALA ASP GLY LYS VAL ASP VAL SEQRES 10 B 175 ILE MET ASN ALA PRO ASP THR SER LEU LYS LYS GLY SER SEQRES 11 B 175 LYS LEU ASN ILE LEU ASP GLU ASP GLY SER ALA PHE ILE SEQRES 12 B 175 ILE HIS GLU GLN ALA ASP ASP TYR LEU THR ASN PRO SER SEQRES 13 B 175 GLY ASN SER GLY ALA ARG ILE VAL CYS GLY ALA LEU LEU SEQRES 14 B 175 GLY ASN ASN GLU LYS GLN SEQRES 1 A 175 LYS PRO PRO ASP PRO PRO ASN ARG VAL PRO GLU LYS LYS SEQRES 2 A 175 VAL VAL GLU THR SER ALA PHE GLY HIS HIS VAL GLN LEU SEQRES 3 A 175 VAL ASN ARG GLU GLY LYS ALA VAL GLY PHE ILE GLU ILE SEQRES 4 A 175 LYS GLU SER ASP ASP GLU GLY LEU ASP ILE HIS ILE SER SEQRES 5 A 175 ALA ASN SER LEU ARG PRO GLY ALA SER LEU GLY PHE HIS SEQRES 6 A 175 ILE HIS GLU LYS GLY SER CYS VAL ARG PRO ASP PHE GLU SEQRES 7 A 175 SER ALA GLY GLY HIS PHE ASN PRO LEU ASN LYS GLU HIS SEQRES 8 A 175 GLY PHE ASN ASN PRO MET GLY HIS HIS ALA GLY ASP LEU SEQRES 9 A 175 PRO ASN LEU GLU VAL GLY ALA ASP GLY LYS VAL ASP VAL SEQRES 10 A 175 ILE MET ASN ALA PRO ASP THR SER LEU LYS LYS GLY SER SEQRES 11 A 175 LYS LEU ASN ILE LEU ASP GLU ASP GLY SER ALA PHE ILE SEQRES 12 A 175 ILE HIS GLU GLN ALA ASP ASP TYR LEU THR ASN PRO SER SEQRES 13 A 175 GLY ASN SER GLY ALA ARG ILE VAL CYS GLY ALA LEU LEU SEQRES 14 A 175 GLY ASN ASN GLU LYS GLN HET CU B 500 1 HET ZN B 501 1 HET ZN B 502 1 HET ZN B 505 1 HET ZN B 506 1 HET CU A 503 1 HET ZN A 504 1 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION FORMUL 3 CU 2(CU 2+) FORMUL 4 ZN 5(ZN 2+) FORMUL 10 HOH *226(H2 O) HELIX 1 1 PHE B 98 GLY B 102 5 5 SHEET 1 A 7 PHE B 85 HIS B 88 0 SHEET 2 A 7 SER B 161 HIS B 166 -1 O ALA B 162 N HIS B 88 SHEET 3 A 7 ARG B 183 LEU B 189 -1 O LEU B 189 N SER B 161 SHEET 4 A 7 GLY B 42 ASN B 49 -1 N VAL B 48 O CYS B 186 SHEET 5 A 7 ALA B 54 GLU B 62 -1 O ILE B 60 N GLY B 42 SHEET 6 A 7 LEU B 68 ALA B 74 -1 O HIS B 71 N GLU B 59 SHEET 7 A 7 VAL B 136 ALA B 142 -1 O ALA B 142 N LEU B 68 SHEET 1 B 2 SER B 82 LEU B 83 0 SHEET 2 B 2 LEU B 128 GLU B 129 -1 O LEU B 128 N LEU B 83 SHEET 1 C 7 PHE A 85 HIS A 88 0 SHEET 2 C 7 SER A 161 HIS A 166 -1 O ALA A 162 N HIS A 88 SHEET 3 C 7 ARG A 183 LEU A 189 -1 O LEU A 189 N SER A 161 SHEET 4 C 7 GLY A 42 ASN A 49 -1 N VAL A 48 O CYS A 186 SHEET 5 C 7 ALA A 54 GLU A 62 -1 O ILE A 60 N GLY A 42 SHEET 6 C 7 LEU A 68 ALA A 74 -1 O HIS A 71 N GLU A 59 SHEET 7 C 7 VAL A 136 ALA A 142 -1 O MET A 140 N ILE A 70 SHEET 1 D 2 SER A 82 LEU A 83 0 SHEET 2 D 2 LEU A 128 GLU A 129 -1 O LEU A 128 N LEU A 83 SSBOND 1 CYS B 93 CYS B 186 1555 1555 2.04 SSBOND 2 CYS A 93 CYS A 186 1555 1555 2.05 LINK NE2 HIS B 71 ZN ZN B 502 1555 1555 2.17 LINK ND1 HIS B 86 CU CU B 500 1555 1555 2.05 LINK NE2 HIS B 88 CU CU B 500 1555 1555 2.07 LINK O GLU B 89 ZN ZN B 506 1555 1555 2.52 LINK ND1 HIS B 104 ZN ZN B 501 1555 1555 1.97 LINK ND1 HIS B 112 ZN ZN B 501 1555 1555 2.06 LINK NE2 HIS B 120 ZN ZN B 505 1555 1555 2.32 LINK ND1 HIS B 121 ZN ZN B 501 1555 1555 2.03 LINK OD2 ASP B 124 ZN ZN B 501 1555 1555 1.97 LINK OD1 ASP B 137 ZN ZN B 502 1555 1555 1.92 LINK OD2 ASP B 144 ZN ZN B 505 1555 1555 2.24 LINK OD2 ASP B 157 ZN ZN B 506 1555 1555 2.30 LINK OD1 ASP B 157 ZN ZN B 506 1555 1555 2.45 LINK O GLY B 160 ZN ZN B 506 1555 1555 2.50 LINK NE2 HIS B 166 CU CU B 500 1555 1555 2.00 LINK ZN ZN B 502 NE2 HIS A 71 1555 3547 2.19 LINK ZN ZN B 502 OD1 ASP A 137 1555 3547 1.96 LINK ZN ZN B 505 O HOH B 553 1555 1555 2.00 LINK ZN ZN B 505 O HOH B 642 1555 1555 2.01 LINK ZN ZN B 506 O HOH B 628 1555 1555 2.47 LINK ND1 HIS A 86 CU CU A 503 1555 1555 2.41 LINK NE2 HIS A 88 CU CU A 503 1555 1555 2.24 LINK NE2 HIS A 104 CU CU A 503 1555 1555 2.49 LINK ND1 HIS A 104 ZN ZN A 504 1555 1555 2.08 LINK ND1 HIS A 112 ZN ZN A 504 1555 1555 2.14 LINK ND1 HIS A 121 ZN ZN A 504 1555 1555 1.87 LINK OD2 ASP A 124 ZN ZN A 504 1555 1555 2.03 LINK NE2 HIS A 166 CU CU A 503 1555 1555 1.89 CISPEP 1 ASP B 64 ASP B 65 0 8.99 CISPEP 2 ASP B 65 GLU B 66 0 -12.00 CISPEP 3 ARG B 95 PRO B 96 0 -5.16 CISPEP 4 GLY B 119 HIS B 120 0 2.63 CISPEP 5 ASN B 175 PRO B 176 0 -10.09 CISPEP 6 ASP A 64 ASP A 65 0 2.31 CISPEP 7 ASP A 65 GLU A 66 0 -19.80 CISPEP 8 ARG A 95 PRO A 96 0 2.02 CISPEP 9 SER A 100 ALA A 101 0 -16.36 CISPEP 10 ALA A 101 GLY A 102 0 -26.77 CISPEP 11 GLY A 102 GLY A 103 0 17.75 CISPEP 12 ASN A 175 PRO A 176 0 -11.91 SITE 1 AC1 5 HIS B 86 HIS B 88 HIS B 104 HIS B 166 SITE 2 AC1 5 HOH B 508 SITE 1 AC2 4 HIS B 104 HIS B 112 HIS B 121 ASP B 124 SITE 1 AC3 4 HIS A 71 ASP A 137 HIS B 71 ASP B 137 SITE 1 AC4 4 HIS A 86 HIS A 88 HIS A 104 HIS A 166 SITE 1 AC5 4 HIS A 104 HIS A 112 HIS A 121 ASP A 124 SITE 1 AC6 4 HIS B 120 ASP B 144 HOH B 553 HOH B 642 SITE 1 AC7 5 GLU B 89 ASP B 157 ASP B 159 GLY B 160 SITE 2 AC7 5 HOH B 628 CRYST1 52.462 104.350 58.756 90.00 90.00 90.00 P 21 21 2 8 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 0.019061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017020 0.00000