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- PDB-4h8q: Structure of the Q29T IsdX2-NEAT5 mutant in complex with heme -

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Basic information

Entry
Database: PDB / ID: 4h8q
TitleStructure of the Q29T IsdX2-NEAT5 mutant in complex with heme
ComponentsIron Transport-associated domain protein
KeywordsHEME-BINDING PROTEIN / NEAT domain / Heme transport Heme scavenging / 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: 1.7 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 1.2Sep 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 / software / 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 / _software.name / _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: Iron Transport-associated domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3623
Polymers14,6801
Non-polymers6822
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.090, 109.090, 109.090
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: 14679.691 Da / Num. of mol.: 1 / Fragment: NEAT5 domain, UNP residues 675-797 / Mutation: Q29T
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.: 130 / 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: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 5% PEG 3000, 0.2 M Zn acetate and 0.1 M sodium acetate pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 12, 2012
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→38.57 Å / Num. obs: 35031 / % possible obs: 100 % / Redundancy: 44.5 % / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H8P

4h8p


Resolution: 1.7→38.569 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 1362 5.7 %
Rwork0.1898 --
obs0.1909 23875 99.97 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.616 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 44 130 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061037
X-RAY DIFFRACTIONf_angle_d1.0561409
X-RAY DIFFRACTIONf_dihedral_angle_d15.706378
X-RAY DIFFRACTIONf_chiral_restr0.069147
X-RAY DIFFRACTIONf_plane_restr0.003175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.76120.21561340.20242234X-RAY DIFFRACTION100
1.7612-1.83170.27221330.20382218X-RAY DIFFRACTION100
1.8317-1.9150.19971350.19312242X-RAY DIFFRACTION100
1.915-2.0160.18851370.19072236X-RAY DIFFRACTION100
2.016-2.14230.23741380.18652246X-RAY DIFFRACTION1.01
2.1423-2.30770.23151340.20092217X-RAY DIFFRACTION100
2.3077-2.53990.20591310.21152264X-RAY DIFFRACTION100
2.5399-2.90730.21881400.20162247X-RAY DIFFRACTION100
2.9073-3.66240.23081370.18922272X-RAY DIFFRACTION100
3.6624-38.5790.17311430.17332337X-RAY DIFFRACTION100

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