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- PDB-2hk6: Crystal Structure of B. subtilis ferrochelatase with Iron bound a... -

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Basic information

Entry
Database: PDB / ID: 2hk6
TitleCrystal Structure of B. subtilis ferrochelatase with Iron bound at the active site
ComponentsFerrochelatase
KeywordsLYASE / Heme biosynthesis / Iron / 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
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsAl-Karadaghi, S. / Karlberg, T.
CitationJournal: Biochemistry / Year: 2007
Title: Amino Acid Residues His183 and Glu264 in Bacillus subtilis Ferrochelatase Direct and Facilitate the Insertion of Metal Ion into Protoporphyrin IX
Authors: Hansson, M.D. / Karlberg, T. / Rahardja, M.A. / Al-Karadaghi, S. / Hansson, M.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 Heterogen The authors state that the charge state of FE is unknown.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6868
Polymers35,3901
Non-polymers2967
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.650, 49.980, 118.850
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: 35389.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Plasmid: pLUGT7-H / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32396, EC: 4.99.1.1
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 39.72 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 8
Details: 25% PEG 2000, 0.2 M MgCl2, 0.1 M Tris-HCl , pH 8.0, VAPOR DIFFUSION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0605 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2005
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0605 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 31884 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.027 / Rsym value: 0.055
Reflection shellResolution: 1.7→1.81 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOZ

1doz


Resolution: 1.71→19.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.056 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21951 1595 5 %RANDOM
Rwork0.17609 ---
obs0.17824 30288 100 %-
all-30288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---1.03 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.71→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 24 368 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222574
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9773507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79124.766128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0715442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9771513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021977
X-RAY DIFFRACTIONr_nbd_refined0.20.21236
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2300
X-RAY DIFFRACTIONr_metal_ion_refined0.2610.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.224
X-RAY DIFFRACTIONr_mcbond_it0.8181.51594
X-RAY DIFFRACTIONr_mcangle_it1.29522499
X-RAY DIFFRACTIONr_scbond_it2.26231133
X-RAY DIFFRACTIONr_scangle_it3.4914.51000
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 108 -
Rwork0.211 2048 -
obs--100 %

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