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- PDB-2q3j: Crystal structure of the His183Ala variant of Bacillus subtilis f... -

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Basic information

Entry
Database: PDB / ID: 2q3j
TitleCrystal structure of the His183Ala variant of Bacillus subtilis ferrochelatase in complex with N-Methyl Mesoporphyrin
ComponentsFerrochelatase
KeywordsLYASE / ROSSMANN FOLD / PI-HELIX / N-METHYL MESOPORPHYRIN IX / N-MeMP
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
N-METHYL PROTOPORPHYRIN IX 2,4-DISULFONIC ACID / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKarlberg, T. / Thorvaldsen, O.H. / Al-Karadaghi, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues
Authors: Karlberg, T. / Hansson, M.D. / Yengo, R.K. / Johansson, R. / Thorvaldsen, O.H. / Ferreira, G.C. / Hansson, M. / Al-Karadaghi, S.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7983
Polymers35,1911
Non-polymers6072
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 58.570, 97.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Ferrochelatase / E.C.4.99.1.1 / Protoheme ferro-lyase / Heme synthetase


Mass: 35191.441 Da / Num. of mol.: 1 / Mutation: H183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Plasmid: pH183A / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-H02 / N-METHYL PROTOPORPHYRIN IX 2,4-DISULFONIC ACID / 3,3'-(7,12-DIETHYL-3,8,13,17,22-PENTAMETHYL-22,24-DIHYDROPORPHYRIN-2,18-DIYL)DIPROPANOIC ACID


Mass: 582.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H42N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25-30 % PEG 2000, 0.2 M MgCl2, 0.1 M TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.907
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2005
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. all: 11903 / Num. obs: 11775 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.103 / Rsym value: 0.075 / Net I/σ(I): 18.4
Reflection shellResolution: 2.39→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 10.4 / Num. unique all: 1747 / Rsym value: 0.194 / % possible all: 94

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H1W

2h1w


Resolution: 2.39→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 584 -RANDOM
Rwork0.1829 ---
obs0.1829 11898 97.9 %-
all-11665 --
Refinement stepCycle: LAST / Resolution: 2.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 44 146 2645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_mcbond_it1.3181.5
X-RAY DIFFRACTIONc_mcangle_it2.0962
X-RAY DIFFRACTIONc_scbond_it2.3812
X-RAY DIFFRACTIONc_scangle_it3.5812.5

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