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- PDB-4xzd: Crystal Structure of Wild-type HasA from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 4xzd
TitleCrystal Structure of Wild-type HasA from Yersinia pseudotuberculosis
ComponentsExtracellular heme acquisition hemophore HasA
KeywordsHEME BINDING PROTEIN / heme acquisition system / hemophore
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKanadani, M. / Hino, T. / Nagano, S. / Sato, T. / Ozaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT25291015 Japan
MEXT25410176 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 4, 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 1.3Nov 8, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular heme acquisition hemophore HasA
D: Extracellular heme acquisition hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5314
Polymers47,2982
Non-polymers1,2332
Water9,926551
1
A: Extracellular heme acquisition hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2662
Polymers23,6491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-14 kcal/mol
Surface area8480 Å2
MethodPISA
2
D: Extracellular heme acquisition hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2662
Polymers23,6491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-14 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.740, 53.250, 82.580
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Extracellular heme acquisition hemophore HasA


Mass: 23649.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria)
Strain: IP32953 / Gene: HasA, YPTB0114 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q66G68
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris HCl, 1.1 M Na-citrate, 1.5% 1,6-hexandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.93 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→81.338 Å / Num. all: 45941 / Num. obs: 45941 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.88 Å2 / Rpim(I) all: 0.068 / Rrim(I) all: 0.129 / Rsym value: 0.109 / Net I/av σ(I): 4.929 / Net I/σ(I): 8.1 / Num. measured all: 162443
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.793.60.5551.32389166710.3410.5552.599.7
1.79-1.93.60.391.92265063380.240.393.499.7
1.9-2.033.60.252.92115259050.1540.255.199.7
2.03-2.193.60.1744.11980355540.1070.1746.999.9
2.19-2.43.60.1295.51819451070.080.1298.599.9
2.4-2.693.50.1066.41624946040.0660.1069.999.7
2.69-3.13.50.0877.11421640740.0540.08712.499.7
3.1-3.83.30.0717.71137834820.0460.07115.299.5
3.8-5.383.50.0559.2945626760.0340.05518.199.4
5.38-35.6563.60.0528.6545415300.0320.05217.399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALA3.3.21data reduction
MOLREP11.0.05phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DK0

1dk0


Resolution: 1.7→35.656 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 2386 5.2 %Random selection
Rwork0.1747 ---
obs0.1772 45923 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→35.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 86 551 3379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142902
X-RAY DIFFRACTIONf_angle_d1.6483942
X-RAY DIFFRACTIONf_dihedral_angle_d17.5861036
X-RAY DIFFRACTIONf_chiral_restr0.092392
X-RAY DIFFRACTIONf_plane_restr0.009518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73470.31311140.26362564X-RAY DIFFRACTION100
1.7347-1.77240.28431400.24872555X-RAY DIFFRACTION100
1.7724-1.81370.29871320.24262542X-RAY DIFFRACTION100
1.8137-1.8590.27351530.2432518X-RAY DIFFRACTION99
1.859-1.90930.26351440.22172554X-RAY DIFFRACTION100
1.9093-1.96540.25951510.20552540X-RAY DIFFRACTION100
1.9654-2.02890.25731320.18682563X-RAY DIFFRACTION100
2.0289-2.10140.22641340.18352575X-RAY DIFFRACTION100
2.1014-2.18550.20111300.1732554X-RAY DIFFRACTION100
2.1855-2.2850.26191600.17412528X-RAY DIFFRACTION100
2.285-2.40540.24131410.17032568X-RAY DIFFRACTION100
2.4054-2.55610.21791600.17082529X-RAY DIFFRACTION100
2.5561-2.75340.22051440.17082551X-RAY DIFFRACTION99
2.7534-3.03030.21821310.16352593X-RAY DIFFRACTION100
3.0303-3.46850.18321390.14792569X-RAY DIFFRACTION99
3.4685-4.36870.15941250.13282585X-RAY DIFFRACTION99
4.3687-35.66380.19941560.16042649X-RAY DIFFRACTION100

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