HEADER PROTOHEME FERRO-LYASE 28-MAY-97 1AK1 TITLE FERROCHELATASE FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERROCHELATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTOHEME FERRO-LYASE; COMPND 5 EC: 4.99.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 CELL_LINE: BL21; SOURCE 5 ORGAN: SEED; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 GENE: HEMH; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: BL21; SOURCE 13 EXPRESSION_SYSTEM_GENE: HEMH KEYWDS PROTOHEME FERRO-LYASE, HEME SYNTHESIS, PORPHYRIN, METALLATION, B. KEYWDS 2 SUBTILIS EXPDTA X-RAY DIFFRACTION AUTHOR S.AL-KARADAGHI,M.HANSSON,S.NIKONOV,B.JONSSON,L.HEDERSTEDT REVDAT 3 07-FEB-24 1AK1 1 REMARK REVDAT 2 24-FEB-09 1AK1 1 VERSN REVDAT 1 03-DEC-97 1AK1 0 JRNL AUTH S.AL-KARADAGHI,M.HANSSON,S.NIKONOV,B.JONSSON,L.HEDERSTEDT JRNL TITL CRYSTAL STRUCTURE OF FERROCHELATASE: THE TERMINAL ENZYME IN JRNL TITL 2 HEME BIOSYNTHESIS. JRNL REF STRUCTURE V. 5 1501 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9384565 JRNL DOI 10.1016/S0969-2126(97)00299-2 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 22357 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 SET) : 0.195 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.370 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.25 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.859 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GROW IN 30% PEG 2000, 0.2 M REMARK 280 MGCL2 0.1 M TRIS-HCL, PH 8.5. THESE WERE VORTEXED AND USED AS REMARK 280 SEEDS FOR LARGE SINGLE CRYSTALS IN: 27% PEG 2000, 0.2 M MGCL2, REMARK 280 0.05% NAN3, 0.1 M TRIS-HCL, PH 8.5, SEEDED REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.69500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.69500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.09500 REMARK 290 SMTRY3 4 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 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 1 REMARK 465 SER A 2 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 SER A 121 -84.30 -103.94 REMARK 500 TRP A 147 17.58 -151.83 REMARK 500 ASN A 225 38.21 -74.16 REMARK 500 THR A 226 91.46 19.68 REMARK 500 PRO A 227 -62.69 -100.33 REMARK 500 ASN A 269 -69.93 -104.28 REMARK 500 TYR A 271 -67.03 -109.17 REMARK 500 ASN A 291 -129.50 48.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MAL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: IN THE GOLD AND CADMIUM DERIVATIVES THE METAL REMARK 800 IONS WERE BOUND TO HIS 183. DBREF 1AK1 A 1 310 UNP P32396 HEMH_BACSU 1 310 SEQRES 1 A 310 MET SER ARG LYS LYS MET GLY LEU LEU VAL MET ALA TYR SEQRES 2 A 310 GLY THR PRO TYR LYS GLU GLU ASP ILE GLU ARG TYR TYR SEQRES 3 A 310 THR HIS ILE ARG ARG GLY ARG LYS PRO GLU PRO GLU MET SEQRES 4 A 310 LEU GLN ASP LEU LYS ASP ARG TYR GLU ALA ILE GLY GLY SEQRES 5 A 310 ILE SER PRO LEU ALA GLN ILE THR GLU GLN GLN ALA HIS SEQRES 6 A 310 ASN LEU GLU GLN HIS LEU ASN GLU ILE GLN ASP GLU ILE SEQRES 7 A 310 THR PHE LYS ALA TYR ILE GLY LEU LYS HIS ILE GLU PRO SEQRES 8 A 310 PHE ILE GLU ASP ALA VAL ALA GLU MET HIS LYS ASP GLY SEQRES 9 A 310 ILE THR GLU ALA VAL SER ILE VAL LEU ALA PRO HIS PHE SEQRES 10 A 310 SER THR PHE SER VAL GLN SER TYR ASN LYS ARG ALA LYS SEQRES 11 A 310 GLU GLU ALA GLU LYS LEU GLY GLY LEU THR ILE THR SER SEQRES 12 A 310 VAL GLU SER TRP TYR ASP GLU PRO LYS PHE VAL THR TYR SEQRES 13 A 310 TRP VAL ASP ARG VAL LYS GLU THR TYR ALA SER MET PRO SEQRES 14 A 310 GLU ASP GLU ARG GLU ASN ALA MET LEU ILE VAL SER ALA SEQRES 15 A 310 HIS SER LEU PRO GLU LYS ILE LYS GLU PHE GLY ASP PRO SEQRES 16 A 310 TYR PRO ASP GLN LEU HIS GLU SER ALA LYS LEU ILE ALA SEQRES 17 A 310 GLU GLY ALA GLY VAL SER GLU TYR ALA VAL GLY TRP GLN SEQRES 18 A 310 SER GLU GLY ASN THR PRO ASP PRO TRP LEU GLY PRO ASP SEQRES 19 A 310 VAL GLN ASP LEU THR ARG ASP LEU PHE GLU GLN LYS GLY SEQRES 20 A 310 TYR GLN ALA PHE VAL TYR VAL PRO VAL GLY PHE VAL ALA SEQRES 21 A 310 ASP HIS LEU GLU VAL LEU TYR ASP ASN ASP TYR GLU CYS SEQRES 22 A 310 LYS VAL VAL THR ASP ASP ILE GLY ALA SER TYR TYR ARG SEQRES 23 A 310 PRO GLU MET PRO ASN ALA LYS PRO GLU PHE ILE ASP ALA SEQRES 24 A 310 LEU ALA THR VAL VAL LEU LYS LYS LEU GLY ARG FORMUL 2 HOH *198(H2 O) HELIX 1 1 GLU A 19 ILE A 29 5 11 HELIX 2 2 PRO A 37 ALA A 49 1 13 HELIX 3 3 SER A 54 ILE A 74 1 21 HELIX 4 4 ILE A 93 LYS A 102 1 10 HELIX 5 5 VAL A 122 LEU A 136 1 15 HELIX 6 6 PRO A 151 SER A 167 1 17 HELIX 7 7 GLU A 170 GLU A 174 1 5 HELIX 8 8 GLU A 187 PHE A 192 5 6 HELIX 9 9 TYR A 196 ALA A 211 1 16 HELIX 10 10 VAL A 235 LYS A 246 1 12 HELIX 11 11 LEU A 263 LEU A 266 1 4 HELIX 12 12 GLU A 272 ILE A 280 1 9 HELIX 13 13 PRO A 294 LYS A 307 1 14 SHEET 1 A 4 ILE A 78 LEU A 86 0 SHEET 2 A 4 LYS A 4 ALA A 12 1 N LYS A 4 O THR A 79 SHEET 3 A 4 GLU A 107 VAL A 112 1 N VAL A 109 O GLY A 7 SHEET 4 A 4 THR A 140 SER A 143 1 N THR A 140 O ALA A 108 SHEET 1 B 4 TYR A 216 GLN A 221 0 SHEET 2 B 4 ALA A 176 HIS A 183 1 N LEU A 178 O ALA A 217 SHEET 3 B 4 ALA A 250 VAL A 254 1 N ALA A 250 O MET A 177 SHEET 4 B 4 SER A 283 ARG A 286 1 N SER A 283 O PHE A 251 CISPEP 1 GLU A 90 PRO A 91 0 -0.65 CISPEP 2 GLY A 232 PRO A 233 0 -0.40 SITE 1 MAL 1 HIS A 183 CRYST1 49.390 50.190 120.120 90.00 90.00 90.00 P 21 21 21 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 0.020247 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008325 0.00000