PDB Short entry for 1IX9 HEADER OXIDOREDUCTASE 17-JUN-02 1IX9 TITLE CRYSTAL STRUCTURE OF THE E. COLI MANGANASE(III) SUPEROXIDE DISMUTASE TITLE 2 MUTANT Y174F AT 0.90 ANGSTROMS RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MNSOD; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: QC781; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDT1-5 KEYWDS MANGANESE SUPEROXIDE DISMUTASE, Y174F MUTANT, HYDROGEN BOND, KEYWDS 2 REACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.F.ANDERSON,R.A.EDWARDS,M.M.WHITTAKER,J.W.WHITTAKER,E.N.BAKER, AUTHOR 2 G.B.JAMESON REVDAT 4 25-OCT-23 1IX9 1 REMARK REVDAT 3 10-NOV-21 1IX9 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1IX9 1 VERSN REVDAT 1 17-DEC-02 1IX9 0 JRNL AUTH B.F.ANDERSON,R.A.EDWARDS,M.M.WHITTAKER,J.W.WHITTAKER, JRNL AUTH 2 E.N.BAKER,G.B.JAMESON JRNL TITL STRUCTURES AT 0.90 A RESOLUTION OF THE OXIDISED AND REDUCED JRNL TITL 2 FORMS OF THE Y174F MUTANT OF THE MANGANESE SUPEROXIDE JRNL TITL 3 DISMUTASE FROM ESCHERICHIA COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.A.EDWARDS,M.M.WHITTAKER,J.W.WHITTAKER,E.N.BAKER, REMARK 1 AUTH 2 G.B.JAMESON REMARK 1 TITL REMOVING A HYDROGEN BOND IN THE DIMER INTERFACE OF REMARK 1 TITL 2 ESCHERICHIA COLI MANGANESE SUPEROXIDE DISMUTASE ALTERS REMARK 1 TITL 3 STRUCTURE AND REACTIVITY REMARK 1 REF BIOCHEMISTRY V. 40 4622 2001 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI002403H REMARK 1 REFERENCE 2 REMARK 1 AUTH R.A.EDWARDS,M.M.WHITTAKER,J.W.WHITTAKER,E.N.BAKER, REMARK 1 AUTH 2 G.B.JAMESON REMARK 1 TITL OUTER SPHERE MUTATIONS PERTURB METAL REACTIVITY IN MANGANESE REMARK 1 TITL 2 SUPEROXIDE DISMUTASE REMARK 1 REF BIOCHEMISTRY V. 40 15 2001 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI0018943 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM SHELL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.107 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.107 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2940 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 287367 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.099 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.099 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.119 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2500 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 246699 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3254 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 898 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3982.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2913.7 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 41 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 39676 REMARK 3 NUMBER OF RESTRAINTS : 44548 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.014 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.095 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.097 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.088 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: P.C.MOEWS & R.H.KRETSINGER, J.MOL.BIOL.91(1975)201 REMARK 3 -228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 NO ELECTRON DENSITY IS OBSERVED FOR A SECOND HYDROGEN ATOM ON REMARK 3 THE COORDINATED SOLVENT SPECIES IN EITHER CHAIN. THUS, THE REMARK 3 COORDINATED SOLVENT SPECIES IS ASSIGNED AS A HYDROXIDE ION. REMARK 3 HOWEVER, A SOFT VIBRATIONAL MODE INVOLVING A PUTATIVE SECOND REMARK 3 HYDROGEN ATOM COULD RENDER THIS ATOM UNDETECTABLE IN DIFFERENCE REMARK 3 FOURIER MAPS. REMARK 3 THE CLOSE CONTACTS AND POOR GEOMETRY LISTED IN REMARK 500 REMARK 3 ARE CAUSED BY PARTIAL OCCUPANCIES AND DISORDER. REMARK 4 REMARK 4 1IX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000005369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 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 : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : BENT GERMANIUM SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 287367 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MN-SOD FROM 1IOH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-20% PEG6000, 0.1M BICINE, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.00850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 60 NZ LYS B 68 2.01 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 OG SER B 6 OD2 ASP B 136 2646 2.03 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 A 6 CB SER A 6 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 A 104 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 136 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 180 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 180 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 LYS A 186 CB - CG - CD ANGL. DEV. = 30.9 DEGREES REMARK 500 GLU B 43 CB - CG - CD ANGL. DEV. = 19.6 DEGREES REMARK 500 GLU B 43 OE1 - CD - OE2 ANGL. DEV. = -14.5 DEGREES REMARK 500 LYS B 90 CA - C - N ANGL. DEV. = -15.2 DEGREES REMARK 500 LYS B 90 O - C - N ANGL. DEV. = 15.2 DEGREES REMARK 500 GLU B 115 OE1 - CD - OE2 ANGL. DEV. = -9.4 DEGREES REMARK 500 GLY B 135 N - CA - C ANGL. DEV. = 17.8 DEGREES REMARK 500 GLY B 135 CA - C - N ANGL. DEV. = -33.4 DEGREES REMARK 500 GLY B 135 O - C - N ANGL. DEV. = 28.8 DEGREES REMARK 500 ASP B 136 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 ASP B 136 N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 ASN B 179 N - CA - CB ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG B 180 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 180 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 200 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LYS B 204 CA - C - O ANGL. DEV. = -20.7 DEGREES REMARK 500 LYS B 204 O - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 LYS B 205 C - N - CA ANGL. DEV. = -18.8 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 HIS A 17 -60.12 -91.29 REMARK 500 LYS A 89 143.39 -175.44 REMARK 500 ASN A 145 -128.37 55.34 REMARK 500 TYR A 173 -2.73 -140.78 REMARK 500 GLN A 178 -128.86 57.69 REMARK 500 GLN A 178 -125.14 51.80 REMARK 500 LYS B 29 -69.64 -108.05 REMARK 500 LYS B 89 132.86 -174.68 REMARK 500 ASP B 136 52.64 -6.16 REMARK 500 ASP B 136 18.88 128.27 REMARK 500 ASN B 145 -127.46 56.10 REMARK 500 GLN B 178 -124.13 51.31 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 GLY B 135 ASP B 136 -141.50 REMARK 500 ASP B 136 LYS B 137 147.26 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 MN A 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 81 NE2 90.5 REMARK 620 3 ASP A 167 OD2 85.5 113.8 REMARK 620 4 HIS A 171 NE2 90.7 126.2 119.9 REMARK 620 5 HOH A 676 O 175.1 91.1 89.6 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 81 NE2 90.5 REMARK 620 3 ASP A 167 OD2 85.5 113.8 REMARK 620 4 HIS A 171 NE2 90.7 126.2 119.9 REMARK 620 5 HOH A 676 O 175.1 91.1 89.6 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 26 NE2 REMARK 620 2 HIS B 81 NE2 91.0 REMARK 620 3 ASP B 167 OD2 85.8 114.1 REMARK 620 4 HIS B 171 NE2 90.2 128.1 117.7 REMARK 620 5 HOH B 634 O 175.0 91.7 89.2 91.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 26 NE2 REMARK 620 2 HIS B 81 NE2 91.0 REMARK 620 3 ASP B 167 OD2 85.8 114.1 REMARK 620 4 HIS B 171 NE2 90.2 128.1 117.7 REMARK 620 5 HOH B 634 O 175.0 91.7 89.2 91.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VEW RELATED DB: PDB REMARK 900 1VEW CONTAINS THE NATIVE STRUCTURE OF THE SAME PROTEIN FROM E. COLI REMARK 900 RELATED ID: 1I0H RELATED DB: PDB REMARK 900 1I0H CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN Y174F MUTANT AT REMARK 900 1.35 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 1EN4 RELATED DB: PDB REMARK 900 1EN4 CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN Q146H MUTANT REMARK 900 RELATED ID: 1EN6 RELATED DB: PDB REMARK 900 1EN6 CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN Q146L MUTANT REMARK 900 RELATED ID: 1I08 RELATED DB: PDB REMARK 900 1I08 CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN H30A MUTANT REMARK 900 RELATED ID: 1MMM RELATED DB: PDB REMARK 900 1MMM CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN FE-SUBSTITUTED REMARK 900 RELATED ID: 1IXB RELATED DB: PDB REMARK 900 1IXB CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN REDUCED BY REMARK 900 ADDITION OF 10% H2O2 DBREF 1IX9 A 1 205 UNP P00448 SODM_ECOLI 1 205 DBREF 1IX9 B 1 205 UNP P00448 SODM_ECOLI 1 205 SEQADV 1IX9 PHE A 174 UNP P00448 TYR 174 ENGINEERED MUTATION SEQADV 1IX9 PHE B 174 UNP P00448 TYR 174 ENGINEERED MUTATION SEQRES 1 A 205 SER TYR THR LEU PRO SER LEU PRO TYR ALA TYR ASP ALA SEQRES 2 A 205 LEU GLU PRO HIS PHE ASP LYS GLN THR MET GLU ILE HIS SEQRES 3 A 205 HIS THR LYS HIS HIS GLN THR TYR VAL ASN ASN ALA ASN SEQRES 4 A 205 ALA ALA LEU GLU SER LEU PRO GLU PHE ALA ASN LEU PRO SEQRES 5 A 205 VAL GLU GLU LEU ILE THR LYS LEU ASP GLN LEU PRO ALA SEQRES 6 A 205 ASP LYS LYS THR VAL LEU ARG ASN ASN ALA GLY GLY HIS SEQRES 7 A 205 ALA ASN HIS SER LEU PHE TRP LYS GLY LEU LYS LYS GLY SEQRES 8 A 205 THR THR LEU GLN GLY ASP LEU LYS ALA ALA ILE GLU ARG SEQRES 9 A 205 ASP PHE GLY SER VAL ASP ASN PHE LYS ALA GLU PHE GLU SEQRES 10 A 205 LYS ALA ALA ALA SER ARG PHE GLY SER GLY TRP ALA TRP SEQRES 11 A 205 LEU VAL LEU LYS GLY ASP LYS LEU ALA VAL VAL SER THR SEQRES 12 A 205 ALA ASN GLN ASP SER PRO LEU MET GLY GLU ALA ILE SER SEQRES 13 A 205 GLY ALA SER GLY PHE PRO ILE MET GLY LEU ASP VAL TRP SEQRES 14 A 205 GLU HIS ALA TYR PHE LEU LYS PHE GLN ASN ARG ARG PRO SEQRES 15 A 205 ASP TYR ILE LYS GLU PHE TRP ASN VAL VAL ASN TRP ASP SEQRES 16 A 205 GLU ALA ALA ALA ARG PHE ALA ALA LYS LYS SEQRES 1 B 205 SER TYR THR LEU PRO SER LEU PRO TYR ALA TYR ASP ALA SEQRES 2 B 205 LEU GLU PRO HIS PHE ASP LYS GLN THR MET GLU ILE HIS SEQRES 3 B 205 HIS THR LYS HIS HIS GLN THR TYR VAL ASN ASN ALA ASN SEQRES 4 B 205 ALA ALA LEU GLU SER LEU PRO GLU PHE ALA ASN LEU PRO SEQRES 5 B 205 VAL GLU GLU LEU ILE THR LYS LEU ASP GLN LEU PRO ALA SEQRES 6 B 205 ASP LYS LYS THR VAL LEU ARG ASN ASN ALA GLY GLY HIS SEQRES 7 B 205 ALA ASN HIS SER LEU PHE TRP LYS GLY LEU LYS LYS GLY SEQRES 8 B 205 THR THR LEU GLN GLY ASP LEU LYS ALA ALA ILE GLU ARG SEQRES 9 B 205 ASP PHE GLY SER VAL ASP ASN PHE LYS ALA GLU PHE GLU SEQRES 10 B 205 LYS ALA ALA ALA SER ARG PHE GLY SER GLY TRP ALA TRP SEQRES 11 B 205 LEU VAL LEU LYS GLY ASP LYS LEU ALA VAL VAL SER THR SEQRES 12 B 205 ALA ASN GLN ASP SER PRO LEU MET GLY GLU ALA ILE SER SEQRES 13 B 205 GLY ALA SER GLY PHE PRO ILE MET GLY LEU ASP VAL TRP SEQRES 14 B 205 GLU HIS ALA TYR PHE LEU LYS PHE GLN ASN ARG ARG PRO SEQRES 15 B 205 ASP TYR ILE LYS GLU PHE TRP ASN VAL VAL ASN TRP ASP SEQRES 16 B 205 GLU ALA ALA ALA ARG PHE ALA ALA LYS LYS HET MN A 206 2 HET MN B 206 2 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *898(H2 O) HELIX 1 1 ASP A 19 LYS A 29 1 11 HELIX 2 2 LYS A 29 GLU A 43 1 15 HELIX 3 3 LEU A 45 ASN A 50 1 6 HELIX 4 4 PRO A 52 ILE A 57 1 6 HELIX 5 5 THR A 58 LEU A 63 5 6 HELIX 6 6 PRO A 64 ASP A 66 5 3 HELIX 7 7 LYS A 67 GLY A 87 1 21 HELIX 8 8 GLN A 95 GLY A 107 1 13 HELIX 9 9 SER A 108 ARG A 123 1 16 HELIX 10 10 SER A 148 MET A 151 5 4 HELIX 11 11 GLY A 152 GLY A 157 1 6 HELIX 12 12 TRP A 169 ALA A 172 5 4 HELIX 13 13 TYR A 173 GLN A 178 1 6 HELIX 14 14 ARG A 180 VAL A 192 1 13 HELIX 15 15 ASN A 193 LYS A 205 1 13 HELIX 16 16 ASP B 19 LYS B 29 1 11 HELIX 17 17 LYS B 29 GLU B 43 1 15 HELIX 18 18 LEU B 45 ASN B 50 1 6 HELIX 19 19 PRO B 52 ILE B 57 1 6 HELIX 20 20 THR B 58 LEU B 63 5 6 HELIX 21 21 PRO B 64 ASP B 66 5 3 HELIX 22 22 LYS B 67 GLY B 87 1 21 HELIX 23 23 GLN B 95 GLY B 107 1 13 HELIX 24 24 SER B 108 ARG B 123 1 16 HELIX 25 25 SER B 148 MET B 151 5 4 HELIX 26 26 GLY B 152 GLY B 157 1 6 HELIX 27 27 TRP B 169 ALA B 172 5 4 HELIX 28 28 TYR B 173 GLN B 178 1 6 HELIX 29 29 ARG B 180 TRP B 189 1 10 HELIX 30 30 ASN B 193 LYS B 204 1 12 SHEET 1 A 3 LYS A 137 ALA A 144 0 SHEET 2 A 3 GLY A 127 LYS A 134 -1 N TRP A 130 O VAL A 141 SHEET 3 A 3 PHE A 161 ASP A 167 -1 O LEU A 166 N ALA A 129 SHEET 1 B 3 LYS B 137 ALA B 144 0 SHEET 2 B 3 GLY B 127 LYS B 134 -1 N TRP B 130 O VAL B 141 SHEET 3 B 3 PHE B 161 ASP B 167 -1 O ILE B 163 N LEU B 131 LINK NE2 HIS A 26 MN A MN A 206 1555 1555 2.15 LINK NE2 HIS A 26 MN B MN A 206 1555 1555 2.15 LINK NE2 HIS A 81 MN A MN A 206 1555 1555 2.14 LINK NE2 HIS A 81 MN B MN A 206 1555 1555 2.14 LINK OD2 ASP A 167 MN A MN A 206 1555 1555 2.02 LINK OD2 ASP A 167 MN B MN A 206 1555 1555 2.02 LINK NE2 HIS A 171 MN A MN A 206 1555 1555 2.12 LINK NE2 HIS A 171 MN B MN A 206 1555 1555 2.12 LINK MN A MN A 206 O HOH A 676 1555 1555 2.12 LINK MN B MN A 206 O HOH A 676 1555 1555 2.12 LINK NE2 HIS B 26 MN B MN B 206 1555 1555 2.14 LINK NE2 HIS B 26 MN A MN B 206 1555 1555 2.14 LINK NE2 HIS B 81 MN A MN B 206 1555 1555 2.14 LINK NE2 HIS B 81 MN B MN B 206 1555 1555 2.14 LINK OD2 ASP B 167 MN A MN B 206 1555 1555 2.03 LINK OD2 ASP B 167 MN B MN B 206 1555 1555 2.03 LINK NE2 HIS B 171 MN A MN B 206 1555 1555 2.12 LINK NE2 HIS B 171 MN B MN B 206 1555 1555 2.12 LINK MN A MN B 206 O HOH B 634 1555 1555 2.16 LINK MN B MN B 206 O HOH B 634 1555 1555 2.16 CISPEP 1 GLU A 15 PRO A 16 0 5.04 CISPEP 2 GLU B 15 PRO B 16 0 6.59 SITE 1 AC1 5 HIS A 26 HIS A 81 ASP A 167 HIS A 171 SITE 2 AC1 5 HOH A 676 SITE 1 AC2 5 HIS B 26 HIS B 81 ASP B 167 HIS B 171 SITE 2 AC2 5 HOH B 634 CRYST1 46.893 46.017 95.993 90.00 98.40 90.00 P 1 21 1 4 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 0.021325 0.000000 0.003149 0.00000 SCALE2 0.000000 0.021731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010530 0.00000