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- PDB-1uj8: Structures of ORF3 in Two Crystal Forms, a Member of Isc Machiner... -

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Basic information

Entry
Database: PDB / ID: 1uj8
TitleStructures of ORF3 in Two Crystal Forms, a Member of Isc Machinery of E. coli Involved in the Assembly of Iron-Sulfur Clusters
ComponentsHypothetical protein yfhJ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / IRON-SULFUR CLUSTER / ISC
Function / homology
Function and homology information


iron-sulfur cluster assembly / enzyme inhibitor activity / ferrous iron binding / iron ion binding / cytosol
Similarity search - Function
IscX-like / ISC system FeS cluster assembly, IscX / IscX-like superfamily / Iron-sulphur cluster assembly / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsShimomura, Y. / Takahashi, Y. / Fukuyama, K.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of Escherichia coli YfhJ protein, a member of the ISC machinery involved in assembly of iron-sulfur clusters.
Authors: Shimomura, Y. / Takahashi, Y. / Kakuta, Y. / Fukuyama, K.
History
DepositionJul 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yfhJ


Theoretical massNumber of molelcules
Total (without water)9,0121
Polymers9,0121
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.63, 27.25, 39.68
Angle α, β, γ (deg.)90.00, 111.0, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein yfhJ / ORF3


Mass: 9011.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P0C0L9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B210.9740, 0.9801
SYNCHROTRONSPring-8 BL40B220.75
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 19, 2003
ADSC QUANTUM 42CCDMar 1, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9741
20.98011
30.751
ReflectionResolution: 1.75→20 Å / Num. obs: 7922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.224 / Num. unique all: 795 / Rsym value: 0.224 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→19.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 953146.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 830 10.6 %RANDOM
Rwork0.194 ---
obs-7847 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0279 Å2 / ksol: 0.464872 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.88 Å20 Å2-0.02 Å2
2--3.91 Å20 Å2
3---0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms602 0 0 102 704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 129 10 %
Rwork0.205 1155 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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