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- PDB-1n0i: Crystal Structure of Ferrochelatase with Cadmium bound at active site -

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Basic information

Entry
Database: PDB / ID: 1n0i
TitleCrystal Structure of Ferrochelatase with Cadmium bound at active site
ComponentsFerrochelatase
KeywordsLYASE / 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
: / Coproporphyrin III ferrochelatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLecerof, D. / Fodje, M.N. / Leon, R.A. / Olsson, U. / Hansson, A. / Sigfridsson, E. / Ryde, U. / Hansson, M. / Al-Karadaghi, S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites
Authors: Lecerof, D. / Fodje, M.N. / Leon, R.A. / Olsson, U. / Hansson, A. / Sigfridsson, E. / Ryde, U. / Hansson, M. / Al-Karadaghi, S.
History
DepositionOct 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Revision 1.4Feb 14, 2024Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,7588
Polymers35,3901
Non-polymers3697
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.415, 49.878, 118.777
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) / Production host: Escherichia coli (E. coli) / References: UniProt: P32396, protoporphyrin ferrochelatase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 369 / 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: 39.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: PEG2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Details: Hansson, M., (1995) Proteins: Struct.,Funct., Genet., 23, 607.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.65 mg/mlprotein1drop
22.5 %PEG20001drop
317 mM1dropMgCl2
48 mMTris-HCl1drop
530 %(w/v)PEG20001reservoir
60.2 M1reservoirMgCl2
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.02916 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02916 Å / Relative weight: 1
ReflectionResolution: 2→26.1 Å / Num. all: 19585 / Num. obs: 19585 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.9 Å2
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.258 / Num. unique all: 22104 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 26 Å / Rmerge(I) obs: 0.241
Reflection shell
*PLUS
Lowest resolution: 2.13 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 80

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOZ

1doz


Resolution: 2→26.11 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1918 9.8 %RANDOM
Rwork0.231 ---
obs0.231 19585 97.3 %-
all-20135 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7138 Å2 / ksol: 0.381242 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.74 Å20 Å20 Å2
2---2.98 Å20 Å2
3---8.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→26.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 24 352 2862
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_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2→2.15 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 367 9.7 %
Rwork0.26 2891 -
obs-3828 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MO6.PARAMMO6.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 26 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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