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- PDB-4h8p: NEAT5 domain of IsdX2, a B. anthracis hemophore in complex with heme -

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Basic information

Entry
Database: PDB / ID: 4h8p
TitleNEAT5 domain of IsdX2, a B. anthracis hemophore in complex with heme
ComponentsIron Transport-associated domain protein
KeywordsHEME-BINDING PROTEIN / NEAT domain Near Iron Transport / Heme Transport Heme Acquisition / Hemophore
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Sortase B cell surface sorting signal / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Iron Transport-associated domain protein / Iron Transport-associated domain protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOwens, C.P. / Goulding, C.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Near-iron Transporter (NEAT) Domains of the Anthrax Hemophore IsdX2 Require a Critical Glutamine to Extract Heme from Methemoglobin.
Authors: Honsa, E.S. / Owens, C.P. / Goulding, C.W. / Maresso, A.W.
History
DepositionSep 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Iron Transport-associated domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3893
Polymers14,7071
Non-polymers6822
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.020, 109.020, 109.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Iron Transport-associated domain protein / IsdX2


Mass: 14706.717 Da / Num. of mol.: 1 / Fragment: NEAT5 domain, UNP residues 675-797
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BA_4787, BAS4442, GBAA_4787 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81L45, UniProt: A0A6L8PXZ2*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.85 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG 3000, 0.2 M Zn acetate and 0.1 M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2012
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→54.51 Å / Num. obs: 13751 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.148

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SIK

3sik


Resolution: 2.05→34.475 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1381 10.05 %
Rwork0.1955 --
obs0.1982 13748 99.58 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.884 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 44 99 1093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071023
X-RAY DIFFRACTIONf_angle_d1.2441393
X-RAY DIFFRACTIONf_dihedral_angle_d16.5373
X-RAY DIFFRACTIONf_chiral_restr0.067145
X-RAY DIFFRACTIONf_plane_restr0.004174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11810.21291360.18531213X-RAY DIFFRACTION99
2.1181-2.20290.21821410.19211245X-RAY DIFFRACTION100
2.2029-2.30310.24411360.20071227X-RAY DIFFRACTION100
2.3031-2.42450.26011370.21241229X-RAY DIFFRACTION100
2.4245-2.57640.28311350.21261209X-RAY DIFFRACTION100
2.5764-2.77520.26711410.22621248X-RAY DIFFRACTION1.01
2.7752-3.05430.23241290.21151224X-RAY DIFFRACTION100
3.0543-3.49590.21381430.19821259X-RAY DIFFRACTION100
3.4959-4.40310.21791440.17061248X-RAY DIFFRACTION100
4.4031-34.480.18561390.18971265X-RAY DIFFRACTION97

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