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- PDB-2ovi: Structure of the Heme Binding Protein ChuX -

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Basic information

Entry
Database: PDB / ID: 2ovi
TitleStructure of the Heme Binding Protein ChuX
ComponentsHypothetical protein chuXHypothesis
KeywordsLIGAND BINDING PROTEIN / METAL TRANSPORT / 2 sets of 9 antiparallel beta sheet core flanked by 2 sets of 3 helices and another 2 sets of helices / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologyIntracellular heme transport protein HutX-like / Haem utilisation ChuX/HutX / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / Alpha Beta / Heme utilization carrier protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSuits, M.D.L. / Pal, G.P. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Protein Sci. / Year: 2009
Title: Structure and heme binding properties of Escherichia coli O157:H7 ChuX.
Authors: Suits, M.D. / Lang, J. / Pal, G.P. / Couture, M. / Jia, Z.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A PAIR OF CHUX HOMODIMERS, SUGGESTED FROM THE CRYSTAL STRUCTURE AND SIZE EXCLUSION CHROMATOGRAPHY. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein chuX
B: Hypothetical protein chuX
C: Hypothetical protein chuX
D: Hypothetical protein chuX


Theoretical massNumber of molelcules
Total (without water)73,4114
Polymers73,4114
Non-polymers00
Water6,485360
1
A: Hypothetical protein chuX
D: Hypothetical protein chuX


Theoretical massNumber of molelcules
Total (without water)36,7062
Polymers36,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein chuX
C: Hypothetical protein chuX


Theoretical massNumber of molelcules
Total (without water)36,7062
Polymers36,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.560, 76.560, 140.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is a pair of ChuX homodimers, suggested from the crystal structure and size exclusion chromatography

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Components

#1: Protein
Hypothetical protein chuX / Hypothesis / ShuX-like protein


Mass: 18352.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Species: Escherichia coli / Strain: O157:H7, EDL933, EHEC / Gene: chuX, ECs4384, Z4915 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8X5N5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40 mg/ml protein, equal amount of protein solution and reservoir solution consisting of 1.50 M Ammonium sulfate, 50mM Hepes, pH 7.5, 2% (v/v) PEG 400, crystal appeared after 2-4 days, ...Details: 40 mg/ml protein, equal amount of protein solution and reservoir solution consisting of 1.50 M Ammonium sulfate, 50mM Hepes, pH 7.5, 2% (v/v) PEG 400, crystal appeared after 2-4 days, cryoprotection: Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9795
SYNCHROTRONNSLS X12C21.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 15, 2005
ADSC QUANTUM 3152CCDApr 27, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.11
ReflectionResolution: 2.05→50 Å / Num. obs: 50833 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.055 / Χ2: 0.957 / Net I/σ(I): 15.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.95 / Num. unique all: 5077 / Χ2: 0.701 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97950.47-2.21
13 wavelength20.97970.82-14.27
13 wavelength31.10.63-2.23
Phasing dmFOM : 0.48 / FOM acentric: 0.47 / FOM centric: 0.5 / Reflection: 35240 / Reflection acentric: 34324 / Reflection centric: 916
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-19.9310.640.660.4915811476105
3.9-6.30.490.490.4849584777181
3.1-3.90.460.450.662356067168
2.8-3.10.480.480.6162496109140
2.4-2.80.510.510.531110910898211
2.2-2.40.350.350.2151084997111

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→50 Å / FOM work R set: 0.837 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.25 3137 6.2 %
Rwork0.213 --
obs-47915 94.4 %
Solvent computationBsol: 72.994 Å2
Displacement parametersBiso mean: 49.899 Å2
Baniso -1Baniso -2Baniso -3
1--3.216 Å20 Å20 Å2
2---3.216 Å20 Å2
3---6.432 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 0 360 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it4.3311.5
X-RAY DIFFRACTIONc_scbond_it6.6362
X-RAY DIFFRACTIONc_mcangle_it5.5772
X-RAY DIFFRACTIONc_scangle_it8.3952.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.05-2.060.279650.293780845
2.06-2.080.346590.291773832
2.08-2.090.298590.304784843
2.09-2.110.38570.292798855
2.11-2.120.298490.287813862
2.12-2.140.27530.266833886
2.14-2.160.278400.28769809
2.16-2.170.292650.269870935
2.17-2.190.325620.266847909
2.19-2.210.284490.242822871
2.21-2.230.254620.219843905
2.23-2.250.291610.236881942
2.25-2.270.295590.258838897
2.27-2.290.301620.248886948
2.29-2.310.296540.241908962
2.31-2.330.3640.232863927
2.33-2.350.288480.225894942
2.35-2.380.27750.224831906
2.38-2.40.305570.229915972
2.4-2.430.312660.232859925
2.43-2.460.268670.226907974
2.46-2.490.27660.219874940
2.49-2.520.268770.233901978
2.52-2.550.232500.218930980
2.55-2.580.377600.229896956
2.58-2.620.23570.183897954
2.62-2.660.327660.2269391005
2.66-2.70.25620.21908970
2.7-2.740.312700.229381008
2.74-2.780.247640.212892956
2.78-2.830.31710.2369351006
2.83-2.880.269730.227914987
2.88-2.940.357790.2349221001
2.94-30.241670.228923990
3-3.060.288650.2249601025
3.06-3.130.321630.234898961
3.13-3.210.252610.2359701031
3.21-3.30.315670.2159441011
3.3-3.40.286590.21936995
3.4-3.510.231630.2139541017
3.51-3.630.264720.2179481020
3.63-3.780.234660.1949391005
3.78-3.950.209570.1959431000
3.95-4.160.207770.1889531030
4.16-4.420.152680.1589431011
4.42-4.760.207660.1569651031
4.76-5.230.21610.1799501011
5.23-5.990.268650.229661031
5.99-7.540.231610.2469561017
7.54-500.207710.2139701041
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4hdm_xplor_par.txt

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