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- PDB-1lbq: The crystal structure of Saccharomyces cerevisiae ferrochelatase -

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Basic information

Entry
Database: PDB / ID: 1lbq
TitleThe crystal structure of Saccharomyces cerevisiae ferrochelatase
ComponentsFerrochelatase
KeywordsLYASE / Rossmann Fold / pi-helix
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: 2.4 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
DepositionApr 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1May 5, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrochelatase
B: Ferrochelatase


Theoretical massNumber of molelcules
Total (without water)82,0012
Polymers82,0012
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.610, 97.169, 121.574
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 /


Mass: 41000.727 Da / Num. of mol.: 2 / Fragment: protoheme ferrolyase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P16622, protoporphyrin ferrochelatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
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: 0.96776 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96776 Å / Relative weight: 1
ReflectionResolution: 2.4→19.8 Å / Num. all: 40095 / Num. obs: 40095 / % possible obs: 92.5 % / Observed criterion σ(F): 3 / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.4→2.5 Å / Num. unique all: 4893 / % possible all: 80.9
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 37088
Reflection shell
*PLUS
% possible obs: 80.9 % / Rmerge(I) obs: 0.199

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human ferrochelatase, pdb code: 1hrk

1hrk


Resolution: 2.4→19.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2348 -random
Rwork0.255 ---
all-40095 --
obs-39122 97.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 0 122 5797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.4→2.5 Å
Num. reflection% reflection
Rfree313 -
Rwork4893 -
obs4893 80.9 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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