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- PDB-3tgv: Crystal structure of HutZ,the heme storsge protein from Vibrio ch... -

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Basic information

Entry
Database: PDB / ID: 3tgv
TitleCrystal structure of HutZ,the heme storsge protein from Vibrio cholerae
ComponentsHeme-binding protein HutZ
KeywordsHEME BINDING PROTEIN
Function / homology
Function and homology information


Heme utilization protein HutZ / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
BENZOIC ACID / Heme-binding protein HutZ / Heme-binding protein HutZ
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsLiu, X. / Gong, J. / Wang, Z. / Du, Q. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae
Authors: Liu, X. / Gong, J. / Wang, Z. / Du, Q. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein HutZ
B: Heme-binding protein HutZ
C: Heme-binding protein HutZ
D: Heme-binding protein HutZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7718
Polymers69,2834
Non-polymers4884
Water4,882271
1
A: Heme-binding protein HutZ
B: Heme-binding protein HutZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8864
Polymers34,6412
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-13 kcal/mol
Surface area14250 Å2
MethodPISA
2
C: Heme-binding protein HutZ
D: Heme-binding protein HutZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8864
Polymers34,6412
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-14 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.063, 80.063, 125.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Heme-binding protein HutZ


Mass: 17320.729 Da / Num. of mol.: 4 / Fragment: UNP residues 13-150 / Mutation: H142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: hutZ / Production host: Escherichia coli (E. coli) / References: UniProt: A5F0R4, UniProt: A0A0H3AGE3*PLUS
#2: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M Na/K phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 51132 / Num. obs: 51132 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3925 / Rsym value: 0.474 / % possible all: 73.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VL7

1vl7


Resolution: 1.999→35.805 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / σ(F): 0 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1824 3.91 %RANDOM
Rwork0.1973 ---
all0.1987 46592 --
obs0.1987 46592 87.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.416 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 82.32 Å2 / Biso mean: 34.4221 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-7.6586 Å20 Å2-0 Å2
2--7.6586 Å20 Å2
3----15.3171 Å2
Refinement stepCycle: LAST / Resolution: 1.999→35.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 36 271 4935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074752
X-RAY DIFFRACTIONf_angle_d1.076388
X-RAY DIFFRACTIONf_chiral_restr0.079680
X-RAY DIFFRACTIONf_plane_restr0.004852
X-RAY DIFFRACTIONf_dihedral_angle_d19.1731828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9989-2.05290.2303920.22092333242559
2.0529-2.11330.26041100.2292694280468
2.1133-2.18150.29011170.23212956307375
2.1815-2.25950.24661340.21563329346384
2.2595-2.34990.28471330.20313402353586
2.3499-2.45680.2041410.19973500364189
2.4568-2.58630.2791450.21413550369590
2.5863-2.74830.29051470.22833613376091
2.7483-2.96040.24381620.22133763392596
2.9604-3.25820.2231590.20713834399397
3.2582-3.72920.23781600.18583884404498
3.7292-4.69670.21621640.16163936410099
4.6967-35.8110.20611600.19373974413499

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