HEADER OXIDOREDUCTASE 02-APR-15 4Z5Q TITLE CRYSTAL STRUCTURE OF THE LNMZ CYTOCHROME P450 HYDROXYLASE FROM THE TITLE 2 LEINAMYCIN BIOSYNTHETIC PATHWAY OF STREPTOMYCES ATROOLIVACEUS S-140 TITLE 3 AT 1.8 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES ATROOLIVACEUS; SOURCE 3 ORGANISM_TAXID: 66869; SOURCE 4 STRAIN: S-140; SOURCE 5 GENE: LNMZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF-TEV/LIC KEYWDS HYDROXYLASE, LEINAMYCIN, HEME, MONOOXYGENASE, OXIDOREDUCTASE, KEYWDS 2 STRUCTURAL GENOMICS, PSI-BIOLOGY, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, ENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS, KEYWDS 4 NATPRO EXPDTA X-RAY DIFFRACTION AUTHOR M.MA,J.LOHMAN,J.RUDOLF,M.D.MILLER,H.CAO,J.OSIPIUK,A.JOACHIMIAK, AUTHOR 2 G.N.PHILLIPS JR.,B.SHEN,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (MCSG),ENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS (NATPRO) REVDAT 4 27-SEP-23 4Z5Q 1 HETSYN LINK REVDAT 3 04-DEC-19 4Z5Q 1 REMARK REVDAT 2 20-SEP-17 4Z5Q 1 REMARK REVDAT 1 12-AUG-15 4Z5Q 0 JRNL AUTH M.MA,J.LOHMAN,J.RUDOLF,M.D.MILLER,H.CAO,J.OSIPIUK, JRNL AUTH 2 A.JOACHIMIAK,G.N.PHILLIPS JR.,B.SHEN JRNL TITL CRYSTAL STRUCTURE OF THE LNMZ CYTOCHROME P450 HYDROXYLASE JRNL TITL 2 FROM THE LEINAMYCIN BIOSYNTHETIC PATHWAY OF STREPTOMYCES JRNL TITL 3 ATROOLIVACEUS S-140 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34234 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2392 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2797 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.11000 REMARK 3 B22 (A**2) : -0.64000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.282 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3173 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2984 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4357 ; 1.658 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6871 ; 0.997 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 408 ; 6.057 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;37.466 ;23.431 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 497 ;15.112 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.379 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3659 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 701 ; 0.008 ; 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): 1570 ; 2.955 ; 4.590 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1569 ; 2.955 ; 4.589 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2000 ; 4.449 ; 8.533 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -22 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 30.0880 27.4520 45.3980 REMARK 3 T TENSOR REMARK 3 T11: 0.0252 T22: 0.0799 REMARK 3 T33: 0.0083 T12: 0.0150 REMARK 3 T13: 0.0084 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.3218 L22: 0.2929 REMARK 3 L33: 0.8041 L12: 0.2264 REMARK 3 L13: 0.0165 L23: 0.1573 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.0153 S13: -0.0470 REMARK 3 S21: 0.0212 S22: 0.0269 S23: -0.0216 REMARK 3 S31: 0.0046 S32: 0.1122 S33: 0.0003 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL REMARK 3 B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. REMARK 3 4. THE HEME IRON IS MODELED AS FE2+ AND IS LIKELY REDUCED BY X- REMARK 3 RAY EXPOSURE. 5. DUE TO EVIDENCE OF RADIATION DAMAGE, ONLY THE REMARK 3 FIRST 160 DEGREES OF DATA COLLECTED WERE USED FOR THE FINAL REMARK 3 REFINEMENT DATASET. 6. CHLORIDE, MAGNISIUM AND PEG FRAGMENTS REMARK 3 FROM THE CRYSTLLIZATOION CONDITIONS HAVE BEEN MODELED. REMARK 4 REMARK 4 4Z5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND[111] REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JANUARY 10, 2014 REMARK 200 DATA SCALING SOFTWARE : XDS VERSION JANUARY 10, 2014 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.801 REMARK 200 RESOLUTION RANGE LOW (A) : 46.884 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.83800 REMARK 200 R SYM FOR SHELL (I) : 0.83800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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: PDB ENTRY 2Y98 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS REMARK 280 -TRIS, PH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 41.71700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 GLN A -11 REMARK 465 ASP A -10 REMARK 465 PRO A -9 REMARK 465 GLY A -8 REMARK 465 ASP A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 VAL A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 GLU A 8 REMARK 465 LYS A 9 REMARK 465 THR A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 GLU A 21 REMARK 465 GLY A 22 REMARK 465 LEU A 23 REMARK 465 GLU A 24 REMARK 465 LEU A 25 REMARK 465 SER A 26 REMARK 465 GLN A 27 REMARK 465 SER A 28 REMARK 465 TYR A 29 REMARK 465 ALA A 30 REMARK 465 LYS A 31 REMARK 465 LEU A 32 REMARK 465 PHE A 33 REMARK 465 GLU A 34 REMARK 465 VAL A 382 REMARK 465 GLU A 383 REMARK 465 TRP A 384 REMARK 465 LYS A 385 REMARK 465 ALA A 386 REMARK 465 ASP A 387 REMARK 465 MET A 388 REMARK 465 ILE A 389 REMARK 465 ILE A 390 REMARK 465 ARG A 391 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 ARG A 65 NE CZ NH1 NH2 REMARK 470 ARG A 111 CD NE CZ NH1 NH2 REMARK 470 ARG A 208 CZ NH1 NH2 REMARK 470 GLU A 243 CD OE1 OE2 REMARK 470 ASP A 339 CG OD1 OD2 REMARK 470 ARG A 341 CD NE CZ NH1 NH2 REMARK 470 ARG A 377 CD NE CZ NH1 NH2 REMARK 470 ASP A 381 CA C O CB CG OD1 OD2 REMARK 470 ARG A 394 CD NE CZ NH1 NH2 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 54 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 144 -57.97 -141.90 REMARK 500 ALA A 221 -132.08 65.36 REMARK 500 PHE A 242 -72.10 -82.71 REMARK 500 PHE A 242 -72.23 -82.71 REMARK 500 ARG A 259 65.85 -110.26 REMARK 500 ASP A 269 65.24 -153.99 REMARK 500 ALA A 288 -169.07 -103.66 REMARK 500 ASP A 339 74.25 60.18 REMARK 500 ASN A 340 63.99 -105.50 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 541 DISTANCE = 6.65 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 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 64 OD1 REMARK 620 2 ASP A 163 OD1 80.0 REMARK 620 3 HOH A 544 O 86.8 36.3 REMARK 620 4 HOH A 545 O 170.5 97.5 85.9 REMARK 620 5 HOH A 546 O 84.7 125.5 91.2 89.5 REMARK 620 6 HOH A 547 O 96.1 55.5 89.6 89.8 178.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 198 OD1 REMARK 620 2 HOH A 548 O 95.6 REMARK 620 3 HOH A 549 O 84.9 179.2 REMARK 620 4 HOH A 550 O 85.8 88.7 92.1 REMARK 620 5 HOH A 551 O 93.6 90.9 88.4 179.3 REMARK 620 6 HOH A 552 O 167.5 95.2 84.5 88.0 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 271 OE1 REMARK 620 2 HOH A 553 O 96.8 REMARK 620 3 HOH A 554 O 82.9 179.4 REMARK 620 4 HOH A 555 O 170.6 92.5 87.8 REMARK 620 5 HOH A 556 O 90.5 89.4 91.1 88.4 REMARK 620 6 HOH A 557 O 89.0 90.5 88.9 92.2 179.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 352 SG REMARK 620 2 HEM A 401 NA 96.3 REMARK 620 3 HEM A 401 NB 87.7 90.8 REMARK 620 4 HEM A 401 NC 86.0 177.7 88.8 REMARK 620 5 HEM A 401 ND 94.6 89.1 177.7 91.2 REMARK 620 6 HOH A 409 O 172.7 87.5 86.0 90.1 91.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P33 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NATPRO-GO.120974 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: MCSG-APC109449 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 4Z5P RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG REMARK 999 MGSSHHHHHHSQDPGDENLYFQS. DBREF 4Z5Q A 1 400 UNP Q8GGM6 Q8GGM6_STRAZ 1 400 SEQADV 4Z5Q MET A -22 UNP Q8GGM6 INITIATING METHIONINE SEQADV 4Z5Q GLY A -21 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q SER A -20 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q SER A -19 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -18 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -17 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -16 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -15 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -14 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q HIS A -13 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q SER A -12 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q GLN A -11 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q ASP A -10 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q PRO A -9 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q GLY A -8 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q ASP A -7 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q GLU A -6 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q ASN A -5 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q LEU A -4 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q TYR A -3 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q PHE A -2 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q GLN A -1 UNP Q8GGM6 EXPRESSION TAG SEQADV 4Z5Q SER A 0 UNP Q8GGM6 EXPRESSION TAG SEQRES 1 A 423 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 423 PRO GLY ASP GLU ASN LEU TYR PHE GLN SER MET SER THR SEQRES 3 A 423 GLU VAL GLU THR GLU LYS PRO ALA PRO VAL ALA TYR PRO SEQRES 4 A 423 PHE THR GLY SER GLU GLY LEU GLU LEU SER GLN SER TYR SEQRES 5 A 423 ALA LYS LEU PHE GLU ASP GLY ASP PRO ILE ARG VAL GLN SEQRES 6 A 423 LEU PRO PHE GLY GLU PRO ALA TRP LEU VAL THR ARG TYR SEQRES 7 A 423 ASP ASP ALA ARG PHE VAL LEU THR ASP ARG ARG PHE SER SEQRES 8 A 423 ARG HIS LEU ALA THR GLN ARG ASP GLU PRO ARG MET THR SEQRES 9 A 423 PRO ARG ALA VAL PRO GLU SER ILE LEU THR MET ASP PRO SEQRES 10 A 423 PRO ASP HIS THR ARG LEU ARG THR LEU VAL SER LYS ALA SEQRES 11 A 423 PHE THR PRO ARG ARG ILE GLU SER LYS ARG ALA TRP ILE SEQRES 12 A 423 GLY GLU LEU ALA ALA GLY LEU VAL ALA ASP MET LYS ALA SEQRES 13 A 423 GLY GLY ALA PRO ALA GLU LEU VAL GLY SER TYR ALA LEU SEQRES 14 A 423 ALA ILE PRO VAL THR VAL ILE CYS GLU LEU LEU GLY VAL SEQRES 15 A 423 PRO GLU ASP ASP ARG THR ARG LEU ARG GLY TRP CYS ASP SEQRES 16 A 423 ALA ALA LEU SER THR GLY GLU LEU THR ASP GLU GLU CYS SEQRES 17 A 423 VAL GLN SER PHE MET ASP LEU GLN LYS TYR PHE GLU ASP SEQRES 18 A 423 LEU VAL LYS GLU ARG ARG ALA GLU PRO ARG ASP ASP LEU SEQRES 19 A 423 THR SER ALA LEU ILE GLU ALA ARG ASP ALA HIS ASP ARG SEQRES 20 A 423 LEU ALA GLU PRO GLU LEU ILE GLY LEU CYS ILE SER ILE SEQRES 21 A 423 LEU ILE GLY GLY PHE GLU THR THR ALA SER GLU ILE SER SEQRES 22 A 423 SER PHE VAL HIS VAL LEU GLN GLN ARG ARG GLU LEU TRP SEQRES 23 A 423 THR ARG LEU CYS ALA ASP PRO GLU ALA ILE PRO ALA ALA SEQRES 24 A 423 VAL GLU GLU LEU LEU ARG PHE VAL PRO PHE ALA ALA ASN SEQRES 25 A 423 GLY ILE SER PRO ARG TYR ALA LEU GLU ASP MET THR VAL SEQRES 26 A 423 GLY GLY VAL LEU VAL ARG GLU GLY GLU PRO VAL ILE VAL SEQRES 27 A 423 ASP THR SER ALA VAL ASN ARG ASP GLY LEU VAL PHE ASP SEQRES 28 A 423 ASN ALA ASP GLU VAL VAL ILE ASP ARG ALA ASP ASN ARG SEQRES 29 A 423 HIS MET VAL PHE GLY HIS GLY ALA HIS HIS CYS LEU GLY SEQRES 30 A 423 ALA HIS LEU ALA ARG VAL GLU LEU GLN GLU ALA LEU LYS SEQRES 31 A 423 ALA LEU VAL GLU GLY MET PRO GLY LEU ARG LEU SER GLY SEQRES 32 A 423 ASP VAL GLU TRP LYS ALA ASP MET ILE ILE ARG ALA PRO SEQRES 33 A 423 ARG VAL MET HIS VAL GLU TRP HET HEM A 401 43 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET CL A 405 1 HET CL A 406 1 HET P33 A 407 22 HET 1PE A 408 16 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN HEM HEME HETSYN P33 HEPTAETHYLENE GLYCOL; PEG330 HETSYN 1PE PEG400 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 MG 3(MG 2+) FORMUL 6 CL 2(CL 1-) FORMUL 8 P33 C14 H30 O8 FORMUL 9 1PE C10 H22 O6 FORMUL 10 HOH *154(H2 O) HELIX 1 AA1 ARG A 54 ASP A 64 1 11 HELIX 2 AA2 ARG A 69 ARG A 75 5 7 HELIX 3 AA3 SER A 88 MET A 92 5 5 HELIX 4 AA4 PRO A 95 PHE A 108 1 14 HELIX 5 AA5 THR A 109 SER A 115 1 7 HELIX 6 AA6 LYS A 116 GLY A 135 1 20 HELIX 7 AA7 LEU A 140 TYR A 144 1 5 HELIX 8 AA8 LEU A 146 GLY A 158 1 13 HELIX 9 AA9 PRO A 160 ARG A 166 5 7 HELIX 10 AB1 LEU A 167 SER A 176 1 10 HELIX 11 AB2 THR A 181 GLU A 206 1 26 HELIX 12 AB3 ASP A 210 ALA A 218 1 9 HELIX 13 AB4 ALA A 226 ARG A 259 1 34 HELIX 14 AB5 ARG A 259 ASP A 269 1 11 HELIX 15 AB6 ALA A 272 VAL A 284 1 13 HELIX 16 AB7 ASP A 316 ASN A 321 1 6 HELIX 17 AB8 HIS A 347 HIS A 351 5 5 HELIX 18 AB9 GLY A 354 MET A 373 1 20 SHEET 1 AA1 6 VAL A 13 ALA A 14 0 SHEET 2 AA1 6 ILE A 39 GLN A 42 1 O GLN A 42 N VAL A 13 SHEET 3 AA1 6 ALA A 49 VAL A 52 -1 O ALA A 49 N VAL A 41 SHEET 4 AA1 6 PRO A 312 VAL A 315 1 O ILE A 314 N TRP A 50 SHEET 5 AA1 6 ARG A 294 ALA A 296 -1 N ARG A 294 O VAL A 313 SHEET 6 AA1 6 PHE A 67 SER A 68 -1 N SER A 68 O TYR A 295 SHEET 1 AA2 3 ALA A 138 GLU A 139 0 SHEET 2 AA2 3 HIS A 397 GLU A 399 -1 O VAL A 398 N ALA A 138 SHEET 3 AA2 3 ARG A 377 GLY A 380 -1 N SER A 379 O HIS A 397 SHEET 1 AA3 2 MET A 300 VAL A 302 0 SHEET 2 AA3 2 VAL A 305 VAL A 307 -1 O VAL A 307 N MET A 300 LINK OD1 ASP A 64 MG MG A 402 1555 1555 2.20 LINK OD1 ASP A 163 MG MG A 402 1555 1556 2.09 LINK OD1 ASP A 198 MG MG A 403 1555 1555 2.18 LINK OE1 GLU A 271 MG MG A 404 1555 1555 2.14 LINK SG CYS A 352 FE HEM A 401 1555 1555 2.30 LINK FE HEM A 401 O HOH A 409 1555 1555 2.18 LINK MG MG A 402 O HOH A 544 1555 1555 2.17 LINK MG MG A 402 O HOH A 545 1555 1555 2.17 LINK MG MG A 402 O HOH A 546 1555 1555 2.16 LINK MG MG A 402 O HOH A 547 1555 1555 2.14 LINK MG MG A 403 O HOH A 548 1555 1555 2.17 LINK MG MG A 403 O HOH A 549 1555 1555 2.17 LINK MG MG A 403 O HOH A 550 1555 1555 2.18 LINK MG MG A 403 O HOH A 551 1555 1555 2.16 LINK MG MG A 403 O HOH A 552 1555 1555 2.17 LINK MG MG A 404 O HOH A 553 1555 1555 2.18 LINK MG MG A 404 O HOH A 554 1555 1555 2.17 LINK MG MG A 404 O HOH A 555 1555 1555 2.18 LINK MG MG A 404 O HOH A 556 1555 1555 2.17 LINK MG MG A 404 O HOH A 557 1555 1555 2.17 CISPEP 1 TYR A 15 PRO A 16 0 2.63 CISPEP 2 PRO A 94 PRO A 95 0 6.01 CISPEP 3 ALA A 136 PRO A 137 0 -7.05 CISPEP 4 GLY A 178 GLU A 179 0 -14.49 SITE 1 AC1 23 ILE A 89 LEU A 90 HIS A 97 ARG A 101 SITE 2 AC1 23 PHE A 108 ILE A 237 GLY A 240 GLY A 241 SITE 3 AC1 23 THR A 244 ILE A 291 SER A 292 ARG A 294 SITE 4 AC1 23 VAL A 344 PHE A 345 GLY A 346 HIS A 350 SITE 5 AC1 23 CYS A 352 GLY A 354 LEU A 357 ALA A 358 SITE 6 AC1 23 P33 A 407 HOH A 409 HOH A 422 SITE 1 AC2 6 ASP A 64 ASP A 163 HOH A 544 HOH A 545 SITE 2 AC2 6 HOH A 546 HOH A 547 SITE 1 AC3 6 ASP A 198 HOH A 548 HOH A 549 HOH A 550 SITE 2 AC3 6 HOH A 551 HOH A 552 SITE 1 AC4 6 GLU A 271 HOH A 553 HOH A 554 HOH A 555 SITE 2 AC4 6 HOH A 556 HOH A 557 SITE 1 AC5 2 HIS A 351 ARG A 359 SITE 1 AC6 6 GLN A 187 ARG A 308 MET A 373 PRO A 374 SITE 2 AC6 6 GLY A 375 TRP A 400 SITE 1 AC7 11 GLU A 87 PRO A 228 GLY A 232 SER A 236 SITE 2 AC7 11 GLY A 240 THR A 244 ALA A 268 GLY A 290 SITE 3 AC7 11 HEM A 401 HOH A 409 HOH A 537 SITE 1 AC8 5 TYR A 55 HIS A 342 HIS A 347 GLY A 348 SITE 2 AC8 5 HIS A 351 CRYST1 47.307 83.434 48.192 90.00 97.67 90.00 P 1 21 1 2 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 0.021139 0.000000 0.002847 0.00000 SCALE2 0.000000 0.011986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020938 0.00000