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- PDB-1l8x: Crystal Structure of Ferrochelatase from the Yeast, Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 1l8x
TitleCrystal Structure of Ferrochelatase from the Yeast, Saccharomyces cerevisiae, with Cobalt(II) as the Substrate Ion
ComponentsFerrochelatase
KeywordsLYASE / Ferrochelatase / Heme Biosynthesis / protoheme / Ferro-Lyase / Porphyrin Metallation / Cobalt / Mitochondrial inner membrane protein
Function / homology
Function and homology information


Heme biosynthesis / protoporphyrin ferrochelatase / ferrochelatase activity / Mitochondrial protein degradation / heme biosynthetic process / mitochondrial inner membrane / mitochondrion
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
: / Ferrochelatase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKarlberg, T. / Lecerof, D. / Gora, M. / Silvegren, G. / Labbe-Bois, R. / Hansson, M. / Al-Karadaghi, S.
CitationJournal: Biochemistry / Year: 2002
Title: Metal Binding to Saccharomyces cerevisiae Ferrochelatase
Authors: Karlberg, T. / Lecerof, D. / Gora, M. / Silvegren, G. / Labbe-Bois, R. / Hansson, M. / Al-Karadaghi, S.
History
DepositionMar 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: 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 1.4Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Ferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1194
Polymers82,0012
Non-polymers1182
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-32 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.38, 96.66, 120.70
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: 41000.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HEMZ / Production host: Escherichia coli (E. coli) / References: UniProt: P16622, EC: 4.99.1.1
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG2000, 2-propanol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1droppH8.0
220 %(w/v)glycerol1drop
31 %(w/v)n-octyl-beta-D-glucopyranoside1drop
40.1 MTris-HCl1reservoirpH7.5
523 %(w/v)PEG20001reservoir
610 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9678 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9678 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 22973 / Num. obs: 22973 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.9 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 22.9 / Num. unique all: 1710 / % possible all: 60.9
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.174
Reflection shell
*PLUS
% possible obs: 60.9 % / Mean I/σ(I) obs: 0.302

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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 1HRK

1hrk


Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT USING FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2297 -RANDOM
Rwork0.237 ---
all0.237 25273 --
obs0.237 22973 90.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 2 9 5675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_improper_angle_d1.22
LS refinement shell
Resolution (Å)Num. reflection RfreeRefine-IDNum. reflection obs% reflection obs (%)
2.7-2.9197X-RAY DIFFRACTION197524.5
2.9-3.1261X-RAY DIFFRACTION261334.6
3.1-3.3288X-RAY DIFFRACTION287940.9
3.3-3.6267X-RAY DIFFRACTION267645.2
3.6-4.1243X-RAY DIFFRACTION243346.6
4.1-4.6205X-RAY DIFFRACTION205546.2
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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