HEADER OXIDOREDUCTASE 02-MAR-15 4YIO TITLE X-RAY STRUCTURE OF THE IRON/MANGANESE CAMBIALISTIC SUPEROXIDE TITLE 2 DISMUTASE FROM STREPTOCOCCUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1308; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, CAMBIALISTIC, THERMOPHILIC EXPDTA X-RAY DIFFRACTION AUTHOR I.RUSSO KRAUSS,A.MERLINO,A.PICA,F.SICA REVDAT 2 10-JAN-24 4YIO 1 LINK REVDAT 1 13-JAN-16 4YIO 0 JRNL AUTH I.RUSSO KRAUSS,A.MERLINO,A.PICA,R.RULLO,A.BERTONI,A.CAPASSO, JRNL AUTH 2 M.AMATO,F.RICCITIELLO,E.DE VENDITTIS,F.SICA JRNL TITL FINE TUNING OF METAL-SPECIFIC ACTIVITY IN THE MN-LIKE GROUP JRNL TITL 2 OF CAMBIALISTIC SUPEROXIDE DISMUTASES JRNL REF RSC ADV V. 5 87876 2015 JRNL REFN ESSN 2046-2069 JRNL DOI 10.1039/C5RA13559A REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 27.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 69916 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 : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3741 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) : 4616 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 552 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -1.28000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.383 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3417 ; 0.027 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3157 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4678 ; 2.414 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7293 ; 1.092 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 423 ; 6.223 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;30.199 ;25.417 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;12.634 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;20.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 520 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3864 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 766 ; 0.001 ; 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): 1632 ; 2.280 ; 1.933 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1631 ; 2.276 ; 1.932 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2042 ; 2.922 ; 2.893 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2043 ; 2.923 ; 2.895 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1785 ; 3.936 ; 2.264 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1785 ; 3.929 ; 2.264 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2626 ; 5.538 ; 3.263 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4610 ; 7.621 ;18.352 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4610 ; 7.614 ;18.352 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 4YIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000206811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 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) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3LIO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6-2.0 M AMMONIUM SULPHATE, 3-5% REMARK 280 ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 59.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.25850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.11500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.25850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.11500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.06000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.25850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.11500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.06000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.25850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.11500 REMARK 290 SMTRY3 8 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 458 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 460 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 454 LIES ON A SPECIAL POSITION. 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 MET A 0 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 REMARK 465 MET B 0 REMARK 465 HIS B 202 REMARK 465 HIS B 203 REMARK 465 HIS B 204 REMARK 465 HIS B 205 REMARK 465 HIS B 206 REMARK 465 HIS B 207 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 O1 GOL B 304 O HOH B 401 1.57 REMARK 500 OE2 GLU B 15 O HOH B 677 1.71 REMARK 500 O3 GOL A 306 O HOH A 648 1.71 REMARK 500 OE1 GLU B 198 O HOH B 561 1.75 REMARK 500 OE2 GLU A 90 O HOH A 401 1.76 REMARK 500 O HOH B 495 O HOH B 670 1.78 REMARK 500 O HOH B 571 O HOH B 670 1.89 REMARK 500 OE1 GLU B 194 O HOH B 402 1.91 REMARK 500 OE2 GLU A 21 NH2 ARG B 173 1.98 REMARK 500 OE1 GLU A 15 O HOH A 551 1.98 REMARK 500 C3 GOL A 307 O HOH A 650 2.07 REMARK 500 NH1 ARG A 173 OE2 GLU B 21 2.18 REMARK 500 O HOH A 622 O HOH A 640 2.19 REMARK 500 OE1 GLU A 90 O HOH A 402 2.19 REMARK 500 O HOH A 566 O HOH A 594 2.19 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 461 O HOH B 461 3555 1.78 REMARK 500 O HOH B 416 O HOH B 452 3555 1.90 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 GLU A 194 CG GLU A 194 CD 0.109 REMARK 500 TYR B 9 CZ TYR B 9 CE2 -0.085 REMARK 500 GLU B 97 CG GLU B 97 CD 0.098 REMARK 500 GLU B 97 CD GLU B 97 OE1 0.085 REMARK 500 GLU B 97 CD GLU B 97 OE2 0.070 REMARK 500 GLU B 104 CD GLU B 104 OE1 0.076 REMARK 500 GLU B 198 CG GLU B 198 CD 0.101 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 GLU A 97 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 GLU A 140 OE1 - CD - OE2 ANGL. DEV. = -9.8 DEGREES REMARK 500 TYR A 172 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 TYR A 179 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 GLU A 194 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 LEU B 4 CB - CG - CD2 ANGL. DEV. = 13.1 DEGREES REMARK 500 ASP B 6 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP B 12 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 GLU B 140 OE1 - CD - OE2 ANGL. DEV. = 7.3 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 ASN A 146 -124.31 55.23 REMARK 500 TYR A 168 -10.41 -140.80 REMARK 500 ARG A 173 -131.39 45.97 REMARK 500 LYS B 29 -62.44 -105.53 REMARK 500 ASN B 146 -122.18 57.40 REMARK 500 ARG B 173 -134.17 50.82 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 A 612 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 623 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH B 680 DISTANCE = 5.92 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 80 NE2 92.9 REMARK 620 3 ASP A 162 OD2 84.4 103.5 REMARK 620 4 HIS A 166 NE2 95.3 140.8 115.5 REMARK 620 5 HOH A 462 O 166.5 89.0 82.2 91.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 26 NE2 REMARK 620 2 HIS B 80 NE2 91.5 REMARK 620 3 ASP B 162 OD2 87.8 100.5 REMARK 620 4 HIS B 166 NE2 93.7 138.6 120.7 REMARK 620 5 HOH B 467 O 169.5 89.0 81.8 92.8 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 FE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 307 DBREF 4YIO A 0 199 UNP Q5M4Z1 Q5M4Z1_STRT2 20 219 DBREF 4YIO B 0 199 UNP Q5M4Z1 Q5M4Z1_STRT2 20 219 SEQADV 4YIO LEU A 200 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO GLU A 201 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 202 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 203 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 204 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 205 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 206 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS A 207 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO LEU B 200 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO GLU B 201 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 202 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 203 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 204 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 205 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 206 UNP Q5M4Z1 EXPRESSION TAG SEQADV 4YIO HIS B 207 UNP Q5M4Z1 EXPRESSION TAG SEQRES 1 A 208 MET ALA ILE ILE LEU PRO ASP LEU PRO TYR ALA TYR ASP SEQRES 2 A 208 ALA LEU GLU PRO TYR ILE ASP ALA GLU THR MET THR LEU SEQRES 3 A 208 HIS HIS ASP LYS HIS HIS ALA THR TYR VAL ALA ASN ALA SEQRES 4 A 208 ASN ALA ALA LEU GLU LYS HIS PRO GLU ILE GLY GLU ASP SEQRES 5 A 208 LEU GLU ALA LEU LEU ALA ASP VAL GLU LYS ILE PRO ALA SEQRES 6 A 208 ASP ILE ARG GLN ALA LEU ILE ASN ASN GLY GLY GLY HIS SEQRES 7 A 208 LEU ASN HIS ALA LEU PHE TRP GLU LEU LEU SER PRO GLU SEQRES 8 A 208 LYS GLN GLU PRO THR ALA GLU VAL ALA ALA ALA ILE ASN SEQRES 9 A 208 GLU ALA PHE GLY SER PHE GLU ALA PHE GLN GLU VAL PHE SEQRES 10 A 208 THR THR SER ALA THR THR ARG PHE GLY SER GLY TRP ALA SEQRES 11 A 208 TRP LEU VAL VAL ASN ALA GLU GLY LYS LEU GLU VAL VAL SEQRES 12 A 208 SER THR PRO ASN GLN ASP THR PRO ILE SER ASP GLY LYS SEQRES 13 A 208 LYS PRO ILE LEU ALA LEU ASP VAL TRP GLU HIS ALA TYR SEQRES 14 A 208 TYR LEU LYS TYR ARG ASN VAL ARG PRO ASN TYR ILE LYS SEQRES 15 A 208 ALA PHE PHE GLU ILE ILE ASN TRP ASN LYS VAL ALA GLU SEQRES 16 A 208 LEU TYR ALA GLU ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 208 MET ALA ILE ILE LEU PRO ASP LEU PRO TYR ALA TYR ASP SEQRES 2 B 208 ALA LEU GLU PRO TYR ILE ASP ALA GLU THR MET THR LEU SEQRES 3 B 208 HIS HIS ASP LYS HIS HIS ALA THR TYR VAL ALA ASN ALA SEQRES 4 B 208 ASN ALA ALA LEU GLU LYS HIS PRO GLU ILE GLY GLU ASP SEQRES 5 B 208 LEU GLU ALA LEU LEU ALA ASP VAL GLU LYS ILE PRO ALA SEQRES 6 B 208 ASP ILE ARG GLN ALA LEU ILE ASN ASN GLY GLY GLY HIS SEQRES 7 B 208 LEU ASN HIS ALA LEU PHE TRP GLU LEU LEU SER PRO GLU SEQRES 8 B 208 LYS GLN GLU PRO THR ALA GLU VAL ALA ALA ALA ILE ASN SEQRES 9 B 208 GLU ALA PHE GLY SER PHE GLU ALA PHE GLN GLU VAL PHE SEQRES 10 B 208 THR THR SER ALA THR THR ARG PHE GLY SER GLY TRP ALA SEQRES 11 B 208 TRP LEU VAL VAL ASN ALA GLU GLY LYS LEU GLU VAL VAL SEQRES 12 B 208 SER THR PRO ASN GLN ASP THR PRO ILE SER ASP GLY LYS SEQRES 13 B 208 LYS PRO ILE LEU ALA LEU ASP VAL TRP GLU HIS ALA TYR SEQRES 14 B 208 TYR LEU LYS TYR ARG ASN VAL ARG PRO ASN TYR ILE LYS SEQRES 15 B 208 ALA PHE PHE GLU ILE ILE ASN TRP ASN LYS VAL ALA GLU SEQRES 16 B 208 LEU TYR ALA GLU ALA LEU GLU HIS HIS HIS HIS HIS HIS HET FE A 301 1 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 A 305 5 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET FE B 301 1 HET SO4 B 302 5 HET SO4 B 303 5 HET GOL B 304 6 HET GOL B 305 6 HET GOL B 306 6 HET GOL B 307 6 HETNAM FE FE (III) ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FE 2(FE 3+) FORMUL 4 SO4 6(O4 S 2-) FORMUL 8 GOL 7(C3 H8 O3) FORMUL 18 HOH *552(H2 O) HELIX 1 AA1 ASP A 19 LYS A 29 1 11 HELIX 2 AA2 LYS A 29 LYS A 44 1 16 HELIX 3 AA3 HIS A 45 GLY A 49 5 5 HELIX 4 AA4 ASP A 51 ASP A 58 1 8 HELIX 5 AA5 VAL A 59 ILE A 62 5 4 HELIX 6 AA6 PRO A 63 ASP A 65 5 3 HELIX 7 AA7 ILE A 66 LEU A 86 1 21 HELIX 8 AA8 THR A 95 GLY A 107 1 13 HELIX 9 AA9 SER A 108 ARG A 123 1 16 HELIX 10 AB1 THR A 149 GLY A 154 5 6 HELIX 11 AB2 TRP A 164 ALA A 167 5 4 HELIX 12 AB3 TYR A 168 ARG A 173 1 6 HELIX 13 AB4 VAL A 175 GLU A 185 1 11 HELIX 14 AB5 ASN A 188 GLU A 201 1 14 HELIX 15 AB6 ASP B 19 LYS B 29 1 11 HELIX 16 AB7 LYS B 29 HIS B 45 1 17 HELIX 17 AB8 PRO B 46 GLY B 49 5 4 HELIX 18 AB9 ASP B 51 ASP B 58 1 8 HELIX 19 AC1 VAL B 59 ILE B 62 5 4 HELIX 20 AC2 ILE B 66 LEU B 86 1 21 HELIX 21 AC3 THR B 95 GLY B 107 1 13 HELIX 22 AC4 SER B 108 ARG B 123 1 16 HELIX 23 AC5 THR B 149 GLY B 154 5 6 HELIX 24 AC6 TRP B 164 ALA B 167 5 4 HELIX 25 AC7 TYR B 168 ARG B 173 1 6 HELIX 26 AC8 VAL B 175 ILE B 186 1 12 HELIX 27 AC9 ASN B 188 GLU B 201 1 14 SHEET 1 AA1 3 LEU A 139 PRO A 145 0 SHEET 2 AA1 3 GLY A 127 VAL A 133 -1 N VAL A 132 O GLU A 140 SHEET 3 AA1 3 LYS A 156 ASP A 162 -1 O ILE A 158 N LEU A 131 SHEET 1 AA2 3 LEU B 139 PRO B 145 0 SHEET 2 AA2 3 GLY B 127 VAL B 133 -1 N VAL B 132 O GLU B 140 SHEET 3 AA2 3 LYS B 156 ASP B 162 -1 O ILE B 158 N LEU B 131 LINK NE2 HIS A 26 FE FE A 301 1555 1555 2.16 LINK NE2 HIS A 80 FE FE A 301 1555 1555 2.12 LINK OD2 ASP A 162 FE FE A 301 1555 1555 2.06 LINK NE2 HIS A 166 FE FE A 301 1555 1555 2.08 LINK FE FE A 301 O HOH A 462 1555 1555 2.30 LINK NE2 HIS B 26 FE FE B 301 1555 1555 2.09 LINK NE2 HIS B 80 FE FE B 301 1555 1555 2.09 LINK OD2 ASP B 162 FE FE B 301 1555 1555 1.96 LINK NE2 HIS B 166 FE FE B 301 1555 1555 2.11 LINK FE FE B 301 O HOH B 467 1555 1555 2.35 CISPEP 1 GLU A 15 PRO A 16 0 11.06 CISPEP 2 GLU A 15 PRO A 16 0 11.65 CISPEP 3 GLU B 15 PRO B 16 0 3.09 CISPEP 4 GLU B 15 PRO B 16 0 3.11 SITE 1 AC1 5 HIS A 26 HIS A 80 ASP A 162 HIS A 166 SITE 2 AC1 5 HOH A 462 SITE 1 AC2 3 ARG A 123 PRO A 145 HOH A 556 SITE 1 AC3 1 ARG A 67 SITE 1 AC4 5 LYS A 29 HOH A 615 HOH A 616 ASN B 174 SITE 2 AC4 5 VAL B 175 SITE 1 AC5 2 GLU A 140 LYS A 155 SITE 1 AC6 6 ASP A 19 GLU A 21 LEU A 170 LYS A 171 SITE 2 AC6 6 HOH A 648 HOH A 662 SITE 1 AC7 6 ASN A 103 SER A 108 PHE A 109 GLU A 110 SITE 2 AC7 6 HOH A 411 HOH A 650 SITE 1 AC8 4 ALA A 10 TYR A 11 ASP A 12 HOH A 640 SITE 1 AC9 5 HIS B 26 HIS B 80 ASP B 162 HIS B 166 SITE 2 AC9 5 HOH B 467 SITE 1 AD1 4 ARG B 123 PRO B 145 HOH B 514 HOH B 669 SITE 1 AD2 6 GLU A 201 HIS A 202 ARG B 67 HOH B 403 SITE 2 AD2 6 HOH B 405 HOH B 418 SITE 1 AD3 7 SER B 119 VAL B 142 SER B 143 HOH B 401 SITE 2 AD3 7 HOH B 446 HOH B 450 HOH B 481 SITE 1 AD4 5 ALA B 10 TYR B 11 ASP B 12 HOH B 470 SITE 2 AD4 5 HOH B 687 SITE 1 AD5 7 LYS B 91 GLN B 92 PRO B 94 PHE B 184 SITE 2 AD5 7 TRP B 189 HOH B 487 HOH B 584 SITE 1 AD6 6 ASP B 19 GLU B 21 LEU B 170 LYS B 171 SITE 2 AD6 6 HOH B 507 HOH B 646 CRYST1 98.517 100.230 118.120 90.00 90.00 90.00 C 2 2 21 16 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 0.010151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008466 0.00000