HEADER OXIDOREDUCTASE 18-MAR-24 9EPD TITLE DTPAA Y389F 8 FS 10 MICROJOULES XFEL PULSE DATA COLLECTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFERROCHELATASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS; SOURCE 3 ORGANISM_TAXID: 1916; SOURCE 4 GENE: SLI_2602; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C43 KEYWDS PEROXIDASE, HEME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.J.WILLIAMS,R.L.OWEN,J.A.R.WORRALL,M.A.HOUGH REVDAT 1 26-MAR-25 9EPD 0 JRNL AUTH L.J.WILLIAMS,R.L.OWEN,J.A.R.WORRALL,M.A.HOUGH JRNL TITL DTPAA Y389F 8 FS 10 MICROJOULES XFEL PULSE DATA COLLECTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 111068 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5899 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8183 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 428 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 533 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.54000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.994 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5829 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5428 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7940 ; 1.877 ; 1.850 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12433 ; 0.655 ; 1.789 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 734 ; 6.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ; 8.541 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 881 ;12.519 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7248 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1482 ; 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): 2906 ; 4.842 ; 1.533 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2905 ; 4.826 ; 1.532 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3632 ; 6.840 ; 2.760 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3633 ; 6.842 ; 2.761 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2923 ; 6.210 ; 1.806 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2921 ; 6.211 ; 1.806 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4302 ; 8.971 ; 3.169 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6482 ;13.621 ;16.520 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6436 ;13.137 ;16.200 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11257 ; 3.901 ; 3.000 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 9EPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292137006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 294.15 REMARK 200 PH : NULL 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 : ESA REMARK 200 X-RAY GENERATOR MODEL : SWISSFEL ARAMIS BEAMLINE ESA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 129619 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 35.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 71.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 47.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.010 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 (%): 44.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% V/V PEG 3350, 100 MM HEPES PH 7.0, REMARK 280 BATCH MODE, TEMPERATURE 298K 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 34.10000 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: 6940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27010 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 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 LYS A 418 REMARK 465 GLU A 419 REMARK 465 ALA A 420 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 465 LYS B 418 REMARK 465 GLU B 419 REMARK 465 ALA B 420 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 OG SER B 136 O HOH B 601 2.08 REMARK 500 O HOH A 662 O HOH A 782 2.11 REMARK 500 O HOH B 616 O HOH B 740 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 824 O HOH B 881 1554 1.88 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. = -3.0 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 251 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 299 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 371 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 158 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 251 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG B 251 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 251 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 342 NE - CZ - NH1 ANGL. DEV. = 3.4 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 -70.67 -119.58 REMARK 500 ASN A 243 -154.98 -119.85 REMARK 500 VAL A 256 -53.55 -120.55 REMARK 500 ARG A 343 39.50 -142.70 REMARK 500 ARG B 343 44.83 -145.70 REMARK 500 PRO B 402 172.93 -58.02 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 151 0.08 SIDE CHAIN REMARK 500 ARG A 242 0.11 SIDE CHAIN REMARK 500 ARG A 277 0.18 SIDE CHAIN REMARK 500 ARG B 242 0.10 SIDE CHAIN REMARK 500 ARG B 279 0.08 SIDE CHAIN REMARK 500 ARG B 313 0.08 SIDE CHAIN 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 850 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B 882 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 883 DISTANCE = 6.25 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 326 NE2 REMARK 620 2 HEM A 501 NA 93.7 REMARK 620 3 HEM A 501 NB 92.4 88.8 REMARK 620 4 HEM A 501 NC 93.5 172.1 87.8 REMARK 620 5 HEM A 501 ND 95.9 91.2 171.7 91.2 REMARK 620 6 HOH A 699 O 170.8 80.5 80.4 91.9 91.4 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 97.0 REMARK 620 3 HEM B 501 NB 93.6 91.1 REMARK 620 4 HEM B 501 NC 96.8 166.2 87.1 REMARK 620 5 HEM B 501 ND 98.7 88.2 167.7 90.6 REMARK 620 6 HOH B 696 O 170.2 79.9 77.2 86.3 90.6 REMARK 620 N 1 2 3 4 5 DBREF1 9EPD A 48 420 UNP A0A7U9DT46_STRLI DBREF2 9EPD A A0A7U9DT46 48 420 DBREF1 9EPD B 48 420 UNP A0A7U9DT46_STRLI DBREF2 9EPD B A0A7U9DT46 48 420 SEQADV 9EPD PHE A 389 UNP A0A7U9DT4 TYR 389 ENGINEERED MUTATION SEQADV 9EPD PHE B 389 UNP A0A7U9DT4 TYR 389 ENGINEERED MUTATION SEQRES 1 A 373 ASP PRO ALA GLY ALA ASP ALA GLY SER ALA VAL PRO PHE SEQRES 2 A 373 HIS GLY ALA HIS GLN ALA GLY ILE ALA THR PRO VAL GLN SEQRES 3 A 373 ASP ARG LEU HIS PHE ALA ALA PHE ASP VAL THR THR GLU SEQRES 4 A 373 ASP ARG ALA ALA PHE VAL ALA LEU LEU LYS GLU TRP THR SEQRES 5 A 373 ALA ALA ALA ARG ARG LEU THR ALA GLY HIS ALA VAL GLY SEQRES 6 A 373 GLU GLY ALA TYR GLY GLY LEU PRO GLU ALA PRO PRO ASP SEQRES 7 A 373 ASP THR GLY GLU ALA LEU GLY LEU LYS PRO SER ARG LEU SEQRES 8 A 373 THR LEU THR ILE GLY PHE GLY PRO SER LEU PHE THR ARG SEQRES 9 A 373 PHE GLY LEU ALA ASP LEU ARG PRO GLU ALA LEU ALA ASP SEQRES 10 A 373 LEU PRO LYS PHE PRO GLY ASP ASN LEU ASP ARG ALA ARG SEQRES 11 A 373 SER GLY GLY ASP LEU CYS VAL GLN ALA CYS ALA ASP ASP SEQRES 12 A 373 PRO GLN VAL ALA VAL HIS ALA ILE ARG ASN LEU ALA ARG SEQRES 13 A 373 ILE GLY PHE GLY LYS VAL VAL VAL ARG TRP SER GLN LEU SEQRES 14 A 373 GLY PHE GLY LYS THR SER SER THR THR PRO ASP LYS GLN SEQRES 15 A 373 THR PRO ARG ASN LEU LEU GLY PHE LYS ASP GLY THR ARG SEQRES 16 A 373 ASN ILE ALA GLY THR GLU LYS ASP ARG LEU ASP ARG PHE SEQRES 17 A 373 VAL TRP ALA ALA GLU LYS ASP GLY THR PRO TRP MET THR SEQRES 18 A 373 GLY GLY SER TYR LEU VAL ALA ARG ARG ILE ARG MET HIS SEQRES 19 A 373 ILE GLU THR TRP ASP ARG ALA SER LEU GLN GLU GLN GLU SEQRES 20 A 373 ASP VAL PHE GLY ARG ASP LYS GLY GLU GLY ALA PRO VAL SEQRES 21 A 373 GLY LYS ALA LYS GLU ARG ASP GLU PRO PHE LEU LYS ALA SEQRES 22 A 373 MET LYS PRO ASP ALA HIS VAL ARG LEU ALA HIS PRO ASP SEQRES 23 A 373 SER ASN GLY GLY ALA THR LEU LEU ARG ARG GLY TYR SER SEQRES 24 A 373 PHE THR ASP GLY THR ASP GLY LEU GLY ARG LEU ASP ALA SEQRES 25 A 373 GLY LEU PHE PHE LEU ALA TYR GLN ARG ASP ILE ARG THR SEQRES 26 A 373 GLY PHE VAL PRO VAL GLN ARG ASN LEU ALA THR ASP ALA SEQRES 27 A 373 LEU ASN GLU PHE ILE GLN HIS VAL GLY SER ALA VAL PHE SEQRES 28 A 373 ALA VAL PRO PRO GLY VAL ARG ASP ALA ASP ASP TRP TRP SEQRES 29 A 373 GLY SER THR LEU PHE GLY LYS GLU ALA SEQRES 1 B 373 ASP PRO ALA GLY ALA ASP ALA GLY SER ALA VAL PRO PHE SEQRES 2 B 373 HIS GLY ALA HIS GLN ALA GLY ILE ALA THR PRO VAL GLN SEQRES 3 B 373 ASP ARG LEU HIS PHE ALA ALA PHE ASP VAL THR THR GLU SEQRES 4 B 373 ASP ARG ALA ALA PHE VAL ALA LEU LEU LYS GLU TRP THR SEQRES 5 B 373 ALA ALA ALA ARG ARG LEU THR ALA GLY HIS ALA VAL GLY SEQRES 6 B 373 GLU GLY ALA TYR GLY GLY LEU PRO GLU ALA PRO PRO ASP SEQRES 7 B 373 ASP THR GLY GLU ALA LEU GLY LEU LYS PRO SER ARG LEU SEQRES 8 B 373 THR LEU THR ILE GLY PHE GLY PRO SER LEU PHE THR ARG SEQRES 9 B 373 PHE GLY LEU ALA ASP LEU ARG PRO GLU ALA LEU ALA ASP SEQRES 10 B 373 LEU PRO LYS PHE PRO GLY ASP ASN LEU ASP ARG ALA ARG SEQRES 11 B 373 SER GLY GLY ASP LEU CYS VAL GLN ALA CYS ALA ASP ASP SEQRES 12 B 373 PRO GLN VAL ALA VAL HIS ALA ILE ARG ASN LEU ALA ARG SEQRES 13 B 373 ILE GLY PHE GLY LYS VAL VAL VAL ARG TRP SER GLN LEU SEQRES 14 B 373 GLY PHE GLY LYS THR SER SER THR THR PRO ASP LYS GLN SEQRES 15 B 373 THR PRO ARG ASN LEU LEU GLY PHE LYS ASP GLY THR ARG SEQRES 16 B 373 ASN ILE ALA GLY THR GLU LYS ASP ARG LEU ASP ARG PHE SEQRES 17 B 373 VAL TRP ALA ALA GLU LYS ASP GLY THR PRO TRP MET THR SEQRES 18 B 373 GLY GLY SER TYR LEU VAL ALA ARG ARG ILE ARG MET HIS SEQRES 19 B 373 ILE GLU THR TRP ASP ARG ALA SER LEU GLN GLU GLN GLU SEQRES 20 B 373 ASP VAL PHE GLY ARG ASP LYS GLY GLU GLY ALA PRO VAL SEQRES 21 B 373 GLY LYS ALA LYS GLU ARG ASP GLU PRO PHE LEU LYS ALA SEQRES 22 B 373 MET LYS PRO ASP ALA HIS VAL ARG LEU ALA HIS PRO ASP SEQRES 23 B 373 SER ASN GLY GLY ALA THR LEU LEU ARG ARG GLY TYR SER SEQRES 24 B 373 PHE THR ASP GLY THR ASP GLY LEU GLY ARG LEU ASP ALA SEQRES 25 B 373 GLY LEU PHE PHE LEU ALA TYR GLN ARG ASP ILE ARG THR SEQRES 26 B 373 GLY PHE VAL PRO VAL GLN ARG ASN LEU ALA THR ASP ALA SEQRES 27 B 373 LEU ASN GLU PHE ILE GLN HIS VAL GLY SER ALA VAL PHE SEQRES 28 B 373 ALA VAL PRO PRO GLY VAL ARG ASP ALA ASP ASP TRP TRP SEQRES 29 B 373 GLY SER THR LEU PHE GLY LYS GLU ALA 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 *533(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 ASP B 286 1 6 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 ARG A 212 N ALA A 80 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 ALA A 396 N ALA A 275 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 HIS B 77 O ALA B 186 SHEET 4 AA4 4 VAL B 209 PHE B 218 -1 O GLN B 215 N PHE B 78 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 VAL B 400 N SER B 271 LINK NE2 HIS A 326 FE HEM A 501 1555 1555 2.09 LINK FE HEM A 501 O HOH A 699 1555 1555 2.35 LINK NE2 HIS B 326 FE HEM B 501 1555 1555 2.08 LINK FE HEM B 501 O AHOH B 696 1555 1555 2.38 CRYST1 72.720 68.200 74.600 90.00 105.60 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 0.013751 0.000000 0.003839 0.00000 SCALE2 0.000000 0.014663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013918 0.00000