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- PDB-7qxv: Crystal Structure of Haem-Binding Protein HemS Mutant F104A F199A... -

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Basic information

Entry
Database: PDB / ID: 7qxv
TitleCrystal Structure of Haem-Binding Protein HemS Mutant F104A F199A, from Yersinia enterocolitica
ComponentsHemin transport protein
KeywordsMETAL BINDING PROTEIN / iron / haem-degrading enzyme / host-pathogen interactions
Function / homologyHaemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / iron ion transport / DI(HYDROXYETHYL)ETHER / Hemin transport protein
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsBarker, P.D. / Keith, A. / Brear, P. / Wales, D.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal Structure of Haem-Binding Protein HemS Mutant F104A F199A, from Yersinia enterocolitica
Authors: Barker, P.D. / Keith, A. / Brear, P. / Wales, D.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemin transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2142
Polymers39,1081
Non-polymers1061
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area16660 Å2
Unit cell
Length a, b, c (Å)62.028, 69.613, 73.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemin transport protein


Mass: 39107.699 Da / Num. of mol.: 1 / Mutation: F104A F199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: hemS, ERS008652_00918 / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A485DUW7
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM tris-HCl 1.8 M (NH4)2SO4, 2% (w/v) PEG 400 / PH range: 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.67→50.57 Å / Num. obs: 37692 / % possible obs: 100 % / Redundancy: 18.6 % / Rpim(I) all: 0.096 / Rrim(I) all: 0.415 / Net I/σ(I): 5.6 / Num. measured all: 701834
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
1.67-1.717.90.232887184022.13593.925
4.53-50.5917.132.73528320680.020.082

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0P

2j0p


Resolution: 1.67→50.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 13.711 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1668 4.9 %RANDOM
Rwork0.2326 ---
obs0.235 32065 89.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.68 Å2 / Biso mean: 50.554 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å2-0 Å20 Å2
2--6.32 Å2-0 Å2
3----2.95 Å2
Refinement stepCycle: final / Resolution: 1.67→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 7 99 2819
Biso mean--54.53 47.18 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152622
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6433805
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5776006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87723.099171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46315477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7791520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
LS refinement shellResolution: 1.671→1.714 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.865 19 -
Rwork0.705 484 -
all-503 -
obs--18.36 %

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