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- PDB-1c1h: CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1c1h
TitleCRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN
ComponentsFERROCHELATASE
KeywordsLYASE / ROSSMANN FOLD / ALPHA/BETA FOLD / FERROCHELATASE / HEME SYNTHESIS / PORPHYRIN METALLATION / PI-HELIX
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-METHYLMESOPORPHYRIN / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLecerof, D. / Fodje, M. / Hansson, A. / Hansson, M. / Al-Karadaghi, S.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural and mechanistic basis of porphyrin metallation by ferrochelatase.
Authors: Lecerof, D. / Fodje, M. / Hansson, A. / Hansson, M. / Al-Karadaghi, S.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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)35,9953
Polymers35,3901
Non-polymers6052
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.97, 58.68, 98.05
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 / HEME SYNTHETASE


Mass: 35389.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PLUGT7-H / Production host: Escherichia coli (E. coli) / 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
Details: N-METHYL MESOPORPHYRIN IS HOMOLOGOUS TO N-METHYL PROTOPORPHYRIN WHICH HAS BEEN ISOLATED FROM THE LIVER OF MICE TREATED WITH 3,5-DIETHOXYCARBONYL-1,4- DIHYDROCOLLIDINE (DDC).
#3: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 39.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 2000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
21 ,<N-MeMP1drop
330 %(w/v)PEG20001reservoir
40.2 M1reservoirMgCl2
5100 mMTris-HCl1reservoir
60.5 mM1reservoirCuSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 21988 / Num. obs: 21475 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.342 / % possible all: 91.6
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.5refinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.9→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 243314.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: Alternate conformations for residues 33, 120, 121 and 122
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1042 4.9 %RANDOM
Rwork0.181 ---
all0.181 21988 --
obs0.181 21475 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.84 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å20 Å2
2---0.1 Å20 Å2
3----4.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 50 338 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it4.052
X-RAY DIFFRACTIONc_scangle_it6.42.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 158 4.7 %
Rwork0.214 3204 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3M_D_MPP.PARM_MPP.TOP
X-RAY DIFFRACTION4MO6.PARMO6.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.55

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