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- PDB-2ac4: Crystal structure of the His183Cys mutant variant of Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 2ac4
TitleCrystal structure of the His183Cys mutant variant of Bacillus subtilis Ferrochelatase
ComponentsFerrochelatase
KeywordsLYASE / ROSSMANN FOLD / PI-HELIX
Function / homology
Function and homology information


coproporphyrin ferrochelatase / protoporphyrin ferrochelatase activity / heme biosynthetic process / cytoplasm
Similarity search - Function
Rossmann fold - #1400 / Ferrochelatase, active site / Ferrochelatase signature. / Ferrochelatase / Ferrochelatase, C-terminal / Ferrochelatase, N-terminal / Ferrochelatase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShipovskov, S. / Karlberg, T. / Fodje, M. / Hansson, M.D. / Ferreira, G.C. / Hansson, M. / Reimann, C.T. / Al-Karadaghi, S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Metallation of the Transition-state Inhibitor N-methyl Mesoporphyrin by Ferrochelatase: Implications for the Catalytic Reaction Mechanism.
Authors: Shipovskov, S. / Karlberg, T. / Fodje, M. / Hansson, M.D. / Ferreira, G.C. / Hansson, M. / Reimann, C.T. / Al-Karadaghi, S.
History
DepositionJul 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)35,2241
Polymers35,2241
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.700, 49.800, 119.000
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 / Heme synthetase


Mass: 35223.504 Da / Num. of mol.: 1 / Mutation: H183C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Production host: Escherichia coli (E. coli) / References: UniProt: P32396, EC: 4.99.1.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: PEG 2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.094 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.094 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 16999 / Num. obs: 16999 / % possible obs: 97.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.072
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.227 / Num. unique all: 2434 / Rsym value: 0.2 / % possible all: 88.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOZ

1doz


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 237708.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1556 5 %RANDOM
Rwork0.214 ---
obs0.214 16999 97.1 %-
all-17502 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0079 Å2 / ksol: 0.370038 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---2.44 Å20 Å2
3---1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 73 2555
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 231 5.1 %
Rwork0.226 4317 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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