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- PDB-1u9t: Crystal Structure Analysis of ChuS, an E. coli Heme Oxygenase -

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Basic information

Entry
Database: PDB / ID: 1u9t
TitleCrystal Structure Analysis of ChuS, an E. coli Heme Oxygenase
Componentsputative heme/hemoglobin transport protein
KeywordsOXIDOREDUCTASE / Structural Genomics / The Montreal-Kingston Bacterial Structural Genomics Initiative / Structural Repeat / Central Beta Sheet / flanked by Alpha helices / BSGI
Function / homologyHaemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / iron ion transport / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Hemin transporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsSuits, M.D. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Identification of an Escherichia coli O157:H7 heme oxygenase with tandem functional repeats
Authors: Suits, M.D. / Pal, G.P. / Nakatsu, K. / Matte, A. / Cygler, M. / Jia, Z.
History
DepositionAug 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: 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: putative heme/hemoglobin transport protein


Theoretical massNumber of molelcules
Total (without water)40,0521
Polymers40,0521
Non-polymers00
Water6,053336
1
A: putative heme/hemoglobin transport protein

A: putative heme/hemoglobin transport protein


Theoretical massNumber of molelcules
Total (without water)80,1042
Polymers80,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)41.684, 57.880, 59.578
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative heme/hemoglobin transport protein


Mass: 40052.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ChuS / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8X5N8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 1.79 Å3/Da / Density % sol: 30.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-BM10.979499
SYNCHROTRONAPS 17-BM20.98043455, 0.98043455, 0.9642276
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 30, 2003
SBC-32CCDNov 17, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiliconSINGLE WAVELENGTHMx-ray1
2SiliconMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794991
20.980434551
30.96422761
ReflectionResolution: 2→50 Å / Num. all: 14606 / Num. obs: 14606 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 12.4 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.16→41.46 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 518891.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: waters picked at level greater than 2.5
RfactorNum. reflection% reflectionSelection details
Rfree0.283 846 6 %RANDOM
Rwork0.207 ---
obs0.207 14185 92.5 %-
all-12462 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 120.559 Å2 / ksol: 0.383391 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.84 Å20 Å2-4.2 Å2
2---3.53 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.16→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 0 336 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.41.5
X-RAY DIFFRACTIONc_mcangle_it5.932
X-RAY DIFFRACTIONc_scbond_it6.62
X-RAY DIFFRACTIONc_scangle_it8.32.5
LS refinement shellResolution: 2.16→2.28 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 106 6.2 %
Rwork0.308 1613 -
obs--67.2 %
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 DIFFRACTION4hdm_xplor_par.txthdm_xplor_top.txt

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