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- PDB-1ak1: FERROCHELATASE FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1ak1
TitleFERROCHELATASE FROM BACILLUS SUBTILIS
ComponentsFERROCHELATASE
KeywordsPROTOHEME FERRO-LYASE / HEME SYNTHESIS / PORPHYRIN / METALLATION / B. SUBTILIS
Function / homology
Function and homology information


coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Ferrochelatase / Ferrochelatase, active site / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / Ferrochelatase signature. / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsAl-Karadaghi, S. / Hansson, M. / Nikonov, S. / Jonsson, B. / Hederstedt, L.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis.
Authors: Al-Karadaghi, S. / Hansson, M. / Nikonov, S. / Jonsson, B. / Hederstedt, L.
History
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERROCHELATASE


Theoretical massNumber of molelcules
Total (without water)35,3901
Polymers35,3901
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.390, 50.190, 120.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FERROCHELATASE / PROTOHEME FERRO-LYASE


Mass: 35389.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: HEMH / Organ: SEED / Plasmid: BL21 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HEMH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P32396, EC: 4.99.1.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40 %
Crystal growMethod: seeded / pH: 8.5
Details: CRYSTALS GROW IN 30% PEG 2000, 0.2 M MGCL2 0.1 M TRIS-HCL, PH 8.5. THESE WERE VORTEXED AND USED AS SEEDS FOR LARGE SINGLE CRYSTALS IN: 27% PEG 2000, 0.2 M MGCL2, 0.05% NAN3, 0.1 M TRIS-HCL, PH 8.5, seeded
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.65 mg/mlprotein1drop
22.5 %PEG20001drop
317 mM1dropMgCl2
48 mMTris-HCl1drop
530 %(w/v)PEG20001reservoir
60.2 M1reservoirMgCl2
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.859
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.859 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 24332 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.44 / % possible all: 80
Reflection
*PLUS
Num. measured all: 226242 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.364

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -10 %RANDOM
Rwork0.195 ---
obs0.195 22357 92 %-
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 0 198 2677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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