HEADER OXIDOREDUCTASE 24-JUL-23 8PXQ TITLE SFX FERRIC STRUCTURE OF Y389F VARIANT OF A TYPE DYE-DECOLOURISING TITLE 2 PEROXIDASE DTPAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFERROCHELATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEROXIDASE EFEB; COMPND 5 EC: 1.11.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS 1326; SOURCE 3 ORGANISM_TAXID: 1200984; SOURCE 4 GENE: SLI_2602; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HEME PEROXIDASE, DYE-DECOLOURISING PEROXIDASE, FERRIC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.LUCIC,J.A.R.WORRALL,M.A.HOUGH,H.PFALZGRAF REVDAT 1 12-FEB-25 8PXQ 0 JRNL AUTH M.LUCIC,A.THOMPSON,J.A.R.WORRALL,M.A.HOUGH JRNL TITL SFX FERRIC STRUCTURE OF A TYPE DYE-DECOLOURISING PEROXIDASE JRNL TITL 2 DTPAA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 73582 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3803 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5386 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 297 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 361 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.667 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5746 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5073 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7847 ; 1.924 ; 1.668 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11751 ; 0.649 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 732 ; 6.740 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;17.383 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 792 ;13.690 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6882 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1255 ; 0.005 ; 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): 2919 ; 2.240 ; 1.801 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2918 ; 2.219 ; 1.800 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3654 ; 2.927 ; 2.696 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3655 ; 2.929 ; 2.697 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2827 ; 3.339 ; 2.077 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2825 ; 3.340 ; 2.077 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4193 ; 4.779 ; 2.991 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6279 ; 5.225 ;23.049 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6256 ; 5.217 ;22.998 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 8PXQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292132152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL2 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL2 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.13 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 70.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 V/V RATIO OF A SOLUTION CONTAINING REMARK 280 6.2 MG/ML Y389F DTPAA IN 20 MM SODIUM PHOSPHATE, 150 MM NACL PH REMARK 280 7 WITH A PRECIPITANT SOLUTION CONSISTING OF 100 MM HEPES PH 7 REMARK 280 AND 15% PEG 6000 TO GIVE A FINAL VOLUME OF 400 UL., BATCH MODE, REMARK 280 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 34.07000 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: 7000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 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 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 ASP A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 PRO A 9 REMARK 465 ALA A 10 REMARK 465 PRO A 11 REMARK 465 SER A 12 REMARK 465 PRO A 13 REMARK 465 SER A 14 REMARK 465 ARG A 15 REMARK 465 ARG A 16 REMARK 465 SER A 17 REMARK 465 LEU A 18 REMARK 465 ILE A 19 REMARK 465 GLY A 20 REMARK 465 TRP A 21 REMARK 465 GLY A 22 REMARK 465 GLY A 23 REMARK 465 ALA A 24 REMARK 465 GLY A 25 REMARK 465 LEU A 26 REMARK 465 ALA A 27 REMARK 465 LEU A 28 REMARK 465 GLY A 29 REMARK 465 ALA A 30 REMARK 465 ALA A 31 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 ALA A 34 REMARK 465 GLY A 35 REMARK 465 GLY A 36 REMARK 465 ALA A 37 REMARK 465 VAL A 38 REMARK 465 ALA A 39 REMARK 465 MET A 40 REMARK 465 ASP A 41 REMARK 465 ARG A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 ALA A 45 REMARK 465 ASP A 46 REMARK 465 ALA A 47 REMARK 465 ASP A 48 REMARK 465 PRO A 49 REMARK 465 ALA A 50 REMARK 465 GLY A 51 REMARK 465 ALA A 52 REMARK 465 ASP A 53 REMARK 465 ALA A 54 REMARK 465 GLY A 417 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 THR B 4 REMARK 465 ASP B 5 REMARK 465 SER B 6 REMARK 465 PRO B 7 REMARK 465 ALA B 8 REMARK 465 PRO B 9 REMARK 465 ALA B 10 REMARK 465 PRO B 11 REMARK 465 SER B 12 REMARK 465 PRO B 13 REMARK 465 SER B 14 REMARK 465 ARG B 15 REMARK 465 ARG B 16 REMARK 465 SER B 17 REMARK 465 LEU B 18 REMARK 465 ILE B 19 REMARK 465 GLY B 20 REMARK 465 TRP B 21 REMARK 465 GLY B 22 REMARK 465 GLY B 23 REMARK 465 ALA B 24 REMARK 465 GLY B 25 REMARK 465 LEU B 26 REMARK 465 ALA B 27 REMARK 465 LEU B 28 REMARK 465 GLY B 29 REMARK 465 ALA B 30 REMARK 465 ALA B 31 REMARK 465 ALA B 32 REMARK 465 ALA B 33 REMARK 465 ALA B 34 REMARK 465 GLY B 35 REMARK 465 GLY B 36 REMARK 465 ALA B 37 REMARK 465 VAL B 38 REMARK 465 ALA B 39 REMARK 465 MET B 40 REMARK 465 ASP B 41 REMARK 465 ARG B 42 REMARK 465 ALA B 43 REMARK 465 GLY B 44 REMARK 465 ALA B 45 REMARK 465 ASP B 46 REMARK 465 ALA B 47 REMARK 465 ASP B 48 REMARK 465 PRO B 49 REMARK 465 ALA B 50 REMARK 465 GLY B 51 REMARK 465 ALA B 52 REMARK 465 ASP B 53 REMARK 465 ALA B 54 REMARK 465 GLY B 55 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 134 CE NZ REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 ARG A 175 CD NE CZ NH1 NH2 REMARK 470 LYS A 228 CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 ASP A 250 CG OD1 OD2 REMARK 470 ARG A 254 NE CZ NH1 NH2 REMARK 470 LYS A 261 CD CE NZ REMARK 470 GLU A 292 OE2 REMARK 470 LYS A 319 CD CE NZ REMARK 470 LYS A 322 NZ REMARK 470 ARG A 405 CD NE CZ NH1 NH2 REMARK 470 GLU B 113 OE2 REMARK 470 LEU B 119 CG CD1 CD2 REMARK 470 LYS B 134 CE NZ REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 ARG B 175 CD NE CZ NH1 NH2 REMARK 470 LYS B 228 CD CE NZ REMARK 470 LYS B 249 CD CE NZ REMARK 470 GLU B 260 CD OE1 OE2 REMARK 470 LYS B 261 CE NZ REMARK 470 ARG B 287 CZ NH1 NH2 REMARK 470 LYS B 311 CD CE NZ REMARK 470 LYS B 322 NZ REMARK 470 ARG B 356 NE CZ NH1 NH2 REMARK 470 ARG B 405 CZ NH1 NH2 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 OE2 GLU B 97 O HOH B 601 2.07 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 75 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 251 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 299 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 299 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 342 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 75 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 251 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 276 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 342 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 342 NE - CZ - NH2 ANGL. DEV. = -4.8 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 ILE A 68 -69.46 -120.68 REMARK 500 ARG A 242 79.21 -105.17 REMARK 500 ASN A 243 -158.06 -118.29 REMARK 500 ARG A 343 36.87 -146.72 REMARK 500 ASP A 349 55.59 -118.15 REMARK 500 VAL B 256 -54.13 -120.34 REMARK 500 ARG B 343 35.35 -144.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 75 0.13 SIDE CHAIN REMARK 500 ARG A 88 0.25 SIDE CHAIN REMARK 500 ARG A 104 0.08 SIDE CHAIN REMARK 500 ARG A 151 0.10 SIDE CHAIN REMARK 500 ARG A 177 0.18 SIDE CHAIN REMARK 500 ARG A 242 0.09 SIDE CHAIN REMARK 500 ARG A 279 0.08 SIDE CHAIN REMARK 500 ARG A 379 0.15 SIDE CHAIN REMARK 500 ARG B 104 0.09 SIDE CHAIN REMARK 500 ARG B 151 0.12 SIDE CHAIN REMARK 500 ARG B 177 0.11 SIDE CHAIN REMARK 500 ARG B 242 0.09 SIDE CHAIN REMARK 500 ARG B 251 0.12 SIDE CHAIN REMARK 500 ARG B 254 0.09 SIDE CHAIN REMARK 500 ARG B 279 0.11 SIDE CHAIN REMARK 500 ARG B 313 0.08 SIDE CHAIN 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 326 NE2 REMARK 620 2 HEM A 501 NA 90.5 REMARK 620 3 HEM A 501 NB 93.3 88.1 REMARK 620 4 HEM A 501 NC 96.2 173.2 90.2 REMARK 620 5 HEM A 501 ND 96.0 91.7 170.7 88.9 REMARK 620 6 HOH A 700 O 169.2 81.8 79.0 91.5 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 326 NE2 REMARK 620 2 HEM B 501 NA 94.6 REMARK 620 3 HEM B 501 NB 96.1 89.1 REMARK 620 4 HEM B 501 NC 98.9 166.5 88.5 REMARK 620 5 HEM B 501 ND 99.5 87.8 164.3 91.0 REMARK 620 6 HOH B 634 O 167.7 77.0 75.0 89.6 89.3 REMARK 620 N 1 2 3 4 5 DBREF1 8PXQ A 1 417 UNP A0A7U9DT46_STRLI DBREF2 8PXQ A A0A7U9DT46 1 417 DBREF1 8PXQ B 1 417 UNP A0A7U9DT46_STRLI DBREF2 8PXQ B A0A7U9DT46 1 417 SEQADV 8PXQ PHE A 389 UNP A0A7U9DT4 TYR 389 ENGINEERED MUTATION SEQADV 8PXQ PHE B 389 UNP A0A7U9DT4 TYR 389 ENGINEERED MUTATION SEQRES 1 A 417 MET THR ASP THR ASP SER PRO ALA PRO ALA PRO SER PRO SEQRES 2 A 417 SER ARG ARG SER LEU ILE GLY TRP GLY GLY ALA GLY LEU SEQRES 3 A 417 ALA LEU GLY ALA ALA ALA ALA ALA GLY GLY ALA VAL ALA SEQRES 4 A 417 MET ASP ARG ALA GLY ALA ASP ALA ASP PRO ALA GLY ALA SEQRES 5 A 417 ASP ALA GLY SER ALA VAL PRO PHE HIS GLY ALA HIS GLN SEQRES 6 A 417 ALA GLY ILE ALA THR PRO VAL GLN ASP ARG LEU HIS PHE SEQRES 7 A 417 ALA ALA PHE ASP VAL THR THR GLU ASP ARG ALA ALA PHE SEQRES 8 A 417 VAL ALA LEU LEU LYS GLU TRP THR ALA ALA ALA ARG ARG SEQRES 9 A 417 LEU THR ALA GLY HIS ALA VAL GLY GLU GLY ALA TYR GLY SEQRES 10 A 417 GLY LEU PRO GLU ALA PRO PRO ASP ASP THR GLY GLU ALA SEQRES 11 A 417 LEU GLY LEU LYS PRO SER ARG LEU THR LEU THR ILE GLY SEQRES 12 A 417 PHE GLY PRO SER LEU PHE THR ARG PHE GLY LEU ALA ASP SEQRES 13 A 417 LEU ARG PRO GLU ALA LEU ALA ASP LEU PRO LYS PHE PRO SEQRES 14 A 417 GLY ASP ASN LEU ASP ARG ALA ARG SER GLY GLY ASP LEU SEQRES 15 A 417 CYS VAL GLN ALA CYS ALA ASP ASP PRO GLN VAL ALA VAL SEQRES 16 A 417 HIS ALA ILE ARG ASN LEU ALA ARG ILE GLY PHE GLY LYS SEQRES 17 A 417 VAL VAL VAL ARG TRP SER GLN LEU GLY PHE GLY LYS THR SEQRES 18 A 417 SER SER THR THR PRO ASP LYS GLN THR PRO ARG ASN LEU SEQRES 19 A 417 LEU GLY PHE LYS ASP GLY THR ARG ASN ILE ALA GLY THR SEQRES 20 A 417 GLU LYS ASP ARG LEU ASP ARG PHE VAL TRP ALA ALA GLU SEQRES 21 A 417 LYS ASP GLY THR PRO TRP MET THR GLY GLY SER TYR LEU SEQRES 22 A 417 VAL ALA ARG ARG ILE ARG MET HIS ILE GLU THR TRP ASP SEQRES 23 A 417 ARG ALA SER LEU GLN GLU GLN GLU ASP VAL PHE GLY ARG SEQRES 24 A 417 ASP LYS GLY GLU GLY ALA PRO VAL GLY LYS ALA LYS GLU SEQRES 25 A 417 ARG ASP GLU PRO PHE LEU LYS ALA MET LYS PRO ASP ALA SEQRES 26 A 417 HIS VAL ARG LEU ALA HIS PRO ASP SER ASN GLY GLY ALA SEQRES 27 A 417 THR LEU LEU ARG ARG GLY TYR SER PHE THR ASP GLY THR SEQRES 28 A 417 ASP GLY LEU GLY ARG LEU ASP ALA GLY LEU PHE PHE LEU SEQRES 29 A 417 ALA TYR GLN ARG ASP ILE ARG THR GLY PHE VAL PRO VAL SEQRES 30 A 417 GLN ARG ASN LEU ALA THR ASP ALA LEU ASN GLU PHE ILE SEQRES 31 A 417 GLN HIS VAL GLY SER ALA VAL PHE ALA VAL PRO PRO GLY SEQRES 32 A 417 VAL ARG ASP ALA ASP ASP TRP TRP GLY SER THR LEU PHE SEQRES 33 A 417 GLY SEQRES 1 B 417 MET THR ASP THR ASP SER PRO ALA PRO ALA PRO SER PRO SEQRES 2 B 417 SER ARG ARG SER LEU ILE GLY TRP GLY GLY ALA GLY LEU SEQRES 3 B 417 ALA LEU GLY ALA ALA ALA ALA ALA GLY GLY ALA VAL ALA SEQRES 4 B 417 MET ASP ARG ALA GLY ALA ASP ALA ASP PRO ALA GLY ALA SEQRES 5 B 417 ASP ALA GLY SER ALA VAL PRO PHE HIS GLY ALA HIS GLN SEQRES 6 B 417 ALA GLY ILE ALA THR PRO VAL GLN ASP ARG LEU HIS PHE SEQRES 7 B 417 ALA ALA PHE ASP VAL THR THR GLU ASP ARG ALA ALA PHE SEQRES 8 B 417 VAL ALA LEU LEU LYS GLU TRP THR ALA ALA ALA ARG ARG SEQRES 9 B 417 LEU THR ALA GLY HIS ALA VAL GLY GLU GLY ALA TYR GLY SEQRES 10 B 417 GLY LEU PRO GLU ALA PRO PRO ASP ASP THR GLY GLU ALA SEQRES 11 B 417 LEU GLY LEU LYS PRO SER ARG LEU THR LEU THR ILE GLY SEQRES 12 B 417 PHE GLY PRO SER LEU PHE THR ARG PHE GLY LEU ALA ASP SEQRES 13 B 417 LEU ARG PRO GLU ALA LEU ALA ASP LEU PRO LYS PHE PRO SEQRES 14 B 417 GLY ASP ASN LEU ASP ARG ALA ARG SER GLY GLY ASP LEU SEQRES 15 B 417 CYS VAL GLN ALA CYS ALA ASP ASP PRO GLN VAL ALA VAL SEQRES 16 B 417 HIS ALA ILE ARG ASN LEU ALA ARG ILE GLY PHE GLY LYS SEQRES 17 B 417 VAL VAL VAL ARG TRP SER GLN LEU GLY PHE GLY LYS THR SEQRES 18 B 417 SER SER THR THR PRO ASP LYS GLN THR PRO ARG ASN LEU SEQRES 19 B 417 LEU GLY PHE LYS ASP GLY THR ARG ASN ILE ALA GLY THR SEQRES 20 B 417 GLU LYS ASP ARG LEU ASP ARG PHE VAL TRP ALA ALA GLU SEQRES 21 B 417 LYS ASP GLY THR PRO TRP MET THR GLY GLY SER TYR LEU SEQRES 22 B 417 VAL ALA ARG ARG ILE ARG MET HIS ILE GLU THR TRP ASP SEQRES 23 B 417 ARG ALA SER LEU GLN GLU GLN GLU ASP VAL PHE GLY ARG SEQRES 24 B 417 ASP LYS GLY GLU GLY ALA PRO VAL GLY LYS ALA LYS GLU SEQRES 25 B 417 ARG ASP GLU PRO PHE LEU LYS ALA MET LYS PRO ASP ALA SEQRES 26 B 417 HIS VAL ARG LEU ALA HIS PRO ASP SER ASN GLY GLY ALA SEQRES 27 B 417 THR LEU LEU ARG ARG GLY TYR SER PHE THR ASP GLY THR SEQRES 28 B 417 ASP GLY LEU GLY ARG LEU ASP ALA GLY LEU PHE PHE LEU SEQRES 29 B 417 ALA TYR GLN ARG ASP ILE ARG THR GLY PHE VAL PRO VAL SEQRES 30 B 417 GLN ARG ASN LEU ALA THR ASP ALA LEU ASN GLU PHE ILE SEQRES 31 B 417 GLN HIS VAL GLY SER ALA VAL PHE ALA VAL PRO PRO GLY SEQRES 32 B 417 VAL ARG ASP ALA ASP ASP TRP TRP GLY SER THR LEU PHE SEQRES 33 B 417 GLY HET HEM A 501 43 HET HEM B 501 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *361(H2 O) HELIX 1 AA1 ASP A 87 ALA A 107 1 21 HELIX 2 AA2 PRO A 146 ARG A 151 5 6 HELIX 3 AA3 LEU A 154 ARG A 158 5 5 HELIX 4 AA4 ASP A 174 SER A 178 5 5 HELIX 5 AA5 ASP A 190 GLY A 205 1 16 HELIX 6 AA6 GLU A 248 VAL A 256 1 9 HELIX 7 AA7 ALA A 259 GLY A 263 5 5 HELIX 8 AA8 THR A 264 THR A 268 5 5 HELIX 9 AA9 HIS A 281 ARG A 287 1 7 HELIX 10 AB1 SER A 289 GLY A 298 1 10 HELIX 11 AB2 PHE A 317 MET A 321 5 5 HELIX 12 AB3 ALA A 325 HIS A 331 1 7 HELIX 13 AB4 PRO A 332 ASN A 335 5 4 HELIX 14 AB5 ASP A 369 THR A 372 5 4 HELIX 15 AB6 GLY A 373 LEU A 381 1 9 HELIX 16 AB7 ALA A 382 GLU A 388 5 7 HELIX 17 AB8 ASP B 87 ALA B 107 1 21 HELIX 18 AB9 PRO B 146 ARG B 151 5 6 HELIX 19 AC1 LEU B 154 ARG B 158 5 5 HELIX 20 AC2 ASP B 174 SER B 178 5 5 HELIX 21 AC3 ASP B 190 GLY B 205 1 16 HELIX 22 AC4 GLU B 248 VAL B 256 1 9 HELIX 23 AC5 ALA B 259 GLY B 263 5 5 HELIX 24 AC6 THR B 264 THR B 268 5 5 HELIX 25 AC7 HIS B 281 ARG B 287 1 7 HELIX 26 AC8 SER B 289 GLY B 298 1 10 HELIX 27 AC9 PHE B 317 MET B 321 5 5 HELIX 28 AD1 ALA B 325 HIS B 331 1 7 HELIX 29 AD2 PRO B 332 ASN B 335 5 4 HELIX 30 AD3 ASP B 369 THR B 372 5 4 HELIX 31 AD4 GLY B 373 LEU B 381 1 9 HELIX 32 AD5 ALA B 382 GLU B 388 5 7 HELIX 33 AD6 GLY B 412 GLY B 417 1 6 SHEET 1 AA1 4 THR A 139 PHE A 144 0 SHEET 2 AA1 4 LEU A 182 ALA A 188 -1 O GLN A 185 N THR A 141 SHEET 3 AA1 4 ARG A 75 VAL A 83 -1 N PHE A 81 O LEU A 182 SHEET 4 AA1 4 VAL A 209 GLY A 217 -1 O GLN A 215 N PHE A 78 SHEET 1 AA2 4 GLY A 219 LYS A 220 0 SHEET 2 AA2 4 TYR A 345 PHE A 347 -1 O SER A 346 N GLY A 219 SHEET 3 AA2 4 GLY A 360 GLN A 367 -1 O PHE A 362 N TYR A 345 SHEET 4 AA2 4 LEU A 341 ARG A 342 -1 N LEU A 341 O TYR A 366 SHEET 1 AA3 5 GLY A 219 LYS A 220 0 SHEET 2 AA3 5 TYR A 345 PHE A 347 -1 O SER A 346 N GLY A 219 SHEET 3 AA3 5 GLY A 360 GLN A 367 -1 O PHE A 362 N TYR A 345 SHEET 4 AA3 5 SER A 271 MET A 280 -1 N ARG A 276 O PHE A 363 SHEET 5 AA3 5 ILE A 390 VAL A 400 -1 O PHE A 398 N LEU A 273 SHEET 1 AA4 4 THR B 139 PHE B 144 0 SHEET 2 AA4 4 LEU B 182 ALA B 188 -1 O GLN B 185 N THR B 141 SHEET 3 AA4 4 ARG B 75 VAL B 83 -1 N PHE B 81 O LEU B 182 SHEET 4 AA4 4 VAL B 209 PHE B 218 -1 O TRP B 213 N ALA B 80 SHEET 1 AA5 3 LEU B 341 ARG B 342 0 SHEET 2 AA5 3 LEU B 357 GLN B 367 -1 O TYR B 366 N LEU B 341 SHEET 3 AA5 3 TYR B 345 THR B 351 -1 N TYR B 345 O PHE B 362 SHEET 1 AA6 4 LEU B 341 ARG B 342 0 SHEET 2 AA6 4 LEU B 357 GLN B 367 -1 O TYR B 366 N LEU B 341 SHEET 3 AA6 4 SER B 271 MET B 280 -1 N MET B 280 O ALA B 359 SHEET 4 AA6 4 ILE B 390 VAL B 400 -1 O PHE B 398 N LEU B 273 LINK NE2 HIS A 326 FE HEM A 501 1555 1555 2.14 LINK FE HEM A 501 O HOH A 700 1555 1555 2.40 LINK NE2 HIS B 326 FE HEM B 501 1555 1555 2.10 LINK FE HEM B 501 O HOH B 634 1555 1555 2.69 CRYST1 72.567 68.140 74.800 90.00 105.50 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 0.013780 0.000000 0.003822 0.00000 SCALE2 0.000000 0.014676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013874 0.00000