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- PDB-2c8j: CRYSTAL STRUCTURE OF ferrochelatase HemH-1 from Bacillus anthraci... -

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Basic information

Entry
Database: PDB / ID: 2c8j
TitleCRYSTAL STRUCTURE OF ferrochelatase HemH-1 from Bacillus anthracis, str. Ames
ComponentsFERROCHELATASE 1
KeywordsLYASE / FERROCHELATASE / IRON METABOLISM / HEME BIOSYNTHESIS / METAL-BINDING / PORPHYRIN BIOSYNTHESIS
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 1
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMuller, A. / Lebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: To be Published
Title: Crystal Structure of Ferrochelatase Hemh-1 from Bacillus Anthracis, Str. Ames
Authors: Muller, A. / Lebedev, A.A. / Moroz, O.V. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionDec 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERROCHELATASE 1
B: FERROCHELATASE 1


Theoretical massNumber of molelcules
Total (without water)70,7842
Polymers70,7842
Non-polymers00
Water3,027168
1
A: FERROCHELATASE 1


Theoretical massNumber of molelcules
Total (without water)35,3921
Polymers35,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERROCHELATASE 1


Theoretical massNumber of molelcules
Total (without water)35,3921
Polymers35,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.931, 109.927, 59.404
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FERROCHELATASE 1 / ROTOHEME FERRO-LYASE 1 / HEME SYNTHETASE 1 / HEMH-1


Mass: 35392.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81U22, EC: 4.99.1.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE CATALYZES OF THE FERROUS INSERTION INTO PROTOPORPHYRIN IX.

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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: 2.31 Å3/Da / Density % sol: 46.26 %
Crystal growpH: 8.5 / Details: 0.2M MGCL2, 0.1M TRIS PH 8.5, 30% PEG 30K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 18, 2004 / Details: RH COATED SI MIRROR
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→59.4 Å / Num. obs: 32162 / % possible obs: 81.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 0.8 / % possible all: 80.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AK1

1ak1


Resolution: 2.1→59.44 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.878 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1512 4.9 %RANDOM
Rwork0.234 ---
obs0.237 29222 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.87 Å2
2--3.04 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4880 0 0 168 5048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9636796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3965619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42124.386228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50315819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.921524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023838
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.22174
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23397
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3171.53205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.54824988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.75332103
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.144.51808
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.289 1791
Rfree-0
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18890.1502-0.20612.5962-0.00553.43540.0174-0.21410.0490.0754-0.0260.08750.00380.04380.0086-0.23490.0080.0128-0.2025-0.0285-0.161135.22881.51141.8681
22.07910.18080.36982.6053-0.19553.8930.09690.1321-0.0597-0.0558-0.0484-0.04650.15990.1958-0.0485-0.20.02310.0197-0.0638-0.0341-0.167810.0639-1.802932.9413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 311
2X-RAY DIFFRACTION2B2 - 311

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