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- PDB-4y4s: Crystal Structure of Y75A HasA dimer from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 4y4s
TitleCrystal Structure of Y75A HasA dimer from Yersinia pseudotuberculosis
ComponentsExtracellular heme acquisition hemophore HasA
KeywordsHEME BINDING PROTEIN / hemophore / heme acquisition
Function / homology
Function and homology information


Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Extracellular heme acquisition hemophore HasA
Similarity search - Component
Biological speciesYersinia pseudotuberculosis IP 32953 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsHino, T. / Kanadani, M. / Muroki, T. / Ishimaru, Y. / Wada, Y. / Sato, T. / Ozaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT/JSPS25291015 Japan
MEXT/JSPS25410176 Japan
CitationJournal: J.Inorg.Biochem. / Year: 2015
Title: The crystal structure of heme acquisition system A from Yersinia pseudotuberculosis (HasAypt): Roles of the axial ligand Tyr75 and two distal arginines in heme binding
Authors: Kanadani, M. / Sato, T. / Hino, T. / Nagano, S. / Ozaki, S.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular heme acquisition hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2693
Polymers23,5571
Non-polymers7132
Water1,18966
1
A: Extracellular heme acquisition hemophore HasA
hetero molecules

A: Extracellular heme acquisition hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5396
Polymers47,1142
Non-polymers1,4254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11760 Å2
ΔGint-119 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.760, 52.760, 140.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Extracellular heme acquisition hemophore HasA


Mass: 23556.930 Da / Num. of mol.: 1 / Mutation: Y75A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria)
Strain: IP32953 / Gene: HasA, YPTB0114 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q66G68
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0941.05
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1 M Bicine pH 9.0, 1.8 M Ammnonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.4 % / Number: 119936 / Rsym value: 0.076 / D res high: 2.195 Å / D res low: 46.493 Å / Num. obs: 10551 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.9446.4910.0320.03210.7
4.916.9410.0470.04711.6
4.014.9110.0590.05911.4
3.474.0110.0520.05211.7
3.13.4710.0660.06611.4
2.833.110.120.1211.3
2.622.8310.1930.19311.5
2.452.6210.3230.32311.2
2.312.4510.5190.51911.4
2.22.3110.8330.83311.4
ReflectionResolution: 1.75→49.395 Å / Num. all: 20936 / Num. obs: 20936 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 18.6 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Rsym value: 0.094 / Net I/av σ(I): 6.236 / Net I/σ(I): 18.2 / Num. measured all: 260147
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.75-1.847.90.5051.52351829670.1850.5053.699.9
1.84-1.9612.20.4541.73459928400.1340.4545.5100
1.96-2.0913.60.3492.23611226550.0980.3497.7100
2.09-2.2613.70.2313.33388724820.0650.23111.4100
2.26-2.4713.60.1714.43152423140.0480.17114.9100
2.47-2.7713.60.1285.52860321060.0360.12820.3100
2.77-3.213.50.0867.52532818800.0240.08628.3100
3.2-3.9113.30.05710.62136416100.0160.05740.9100
3.91-5.5312.80.04312.81651312930.0120.04351.8100
5.53-32.953110.03117.886997890.010.03153.799.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→32.953 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1069 5.12 %
Rwork0.2033 19795 -
obs0.2051 20864 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.06 Å2 / Biso mean: 27.1671 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.75→32.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 48 66 1291
Biso mean--32.34 28.36 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161255
X-RAY DIFFRACTIONf_angle_d1.6571706
X-RAY DIFFRACTIONf_chiral_restr0.077171
X-RAY DIFFRACTIONf_plane_restr0.009220
X-RAY DIFFRACTIONf_dihedral_angle_d17.686438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7501-1.82970.30671330.288724042537
1.8297-1.92620.29991350.25524012536
1.9262-2.04680.27871230.225124362559
2.0468-2.20490.23451450.200424412586
2.2049-2.42670.23921510.188724152566
2.4267-2.77770.22521330.190524882621
2.7777-3.49890.2491260.198725162642
3.4989-32.95840.20711230.187726942817

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