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- PDB-5exv: Crystal structure of heme binding protein HutX from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 5exv
TitleCrystal structure of heme binding protein HutX from Vibrio cholerae
ComponentsHemin-degrading HemS.ChuX domain protein
KeywordsHEME-BINDING PROTEIN / heme oxygenase
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
Intracellular 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
Similarity search - Domain/homology
Heme utilization cystosolic carrier protein HutX / Intracellular heme transport protein HutX
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.901 Å
AuthorsSekine, Y. / Tanaka, Y. / Uchida, T.
CitationJournal: Biochemistry / Year: 2016
Title: Cytoplasmic Heme-Binding Protein (HutX) from Vibrio cholerae Is an Intracellular Heme Transport Protein for the Heme-Degrading Enzyme, HutZ
Authors: Sekine, Y. / Tanzawa, T. / Tanaka, Y. / Ishimori, K. / Uchida, T.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemin-degrading HemS.ChuX domain protein
B: Hemin-degrading HemS.ChuX domain protein
C: Hemin-degrading HemS.ChuX domain protein
D: Hemin-degrading HemS.ChuX domain protein
E: Hemin-degrading HemS.ChuX domain protein
F: Hemin-degrading HemS.ChuX domain protein


Theoretical massNumber of molelcules
Total (without water)127,4476
Polymers127,4476
Non-polymers00
Water00
1
A: Hemin-degrading HemS.ChuX domain protein
B: Hemin-degrading HemS.ChuX domain protein


Theoretical massNumber of molelcules
Total (without water)42,4822
Polymers42,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-13 kcal/mol
Surface area17240 Å2
MethodPISA
2
C: Hemin-degrading HemS.ChuX domain protein
D: Hemin-degrading HemS.ChuX domain protein


Theoretical massNumber of molelcules
Total (without water)42,4822
Polymers42,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-16 kcal/mol
Surface area16550 Å2
MethodPISA
3
E: Hemin-degrading HemS.ChuX domain protein
F: Hemin-degrading HemS.ChuX domain protein


Theoretical massNumber of molelcules
Total (without water)42,4822
Polymers42,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-12 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.200, 80.880, 111.090
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hemin-degrading HemS.ChuX domain protein / HutX protein / HuvX protein / Putative heme iron utilization protein


Mass: 21241.189 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: hutX / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085SE34, UniProt: Q9KL40*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG400, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→48.66 Å / Num. obs: 23690 / % possible obs: 98.3 % / Redundancy: 3.41 % / Rsym value: 0.108 / Net I/σ(I): 10.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.34 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.901→48.657 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1185 5.01 %
Rwork0.2464 --
obs0.248 23663 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→48.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7856 0 0 0 7856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098036
X-RAY DIFFRACTIONf_angle_d1.31610860
X-RAY DIFFRACTIONf_dihedral_angle_d21.3343002
X-RAY DIFFRACTIONf_chiral_restr0.0551180
X-RAY DIFFRACTIONf_plane_restr0.0051428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9008-3.03280.38541450.31732733X-RAY DIFFRACTION97
3.0328-3.19270.30021460.28782789X-RAY DIFFRACTION98
3.1927-3.39270.28781500.26692816X-RAY DIFFRACTION98
3.3927-3.65450.28971460.2562779X-RAY DIFFRACTION99
3.6545-4.02220.2681490.24752830X-RAY DIFFRACTION99
4.0222-4.60380.2631480.22082818X-RAY DIFFRACTION99
4.6038-5.79880.26271500.23882850X-RAY DIFFRACTION99
5.7988-48.66410.26721510.23172863X-RAY DIFFRACTION98

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