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- PDB-8glo: Haemophilus parainfluenzae Holo HphA -

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Basic information

Entry
Database: PDB / ID: 8glo
TitleHaemophilus parainfluenzae Holo HphA
ComponentsHemophilin
KeywordsMETAL TRANSPORT / Heme Binding / Hemophore / Type XI Secretion System Cargo / Beta Barrel
Function / homologyHEME B/C
Function and homology information
Biological speciesHaemophilus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å
AuthorsShin, H.E. / Ng, D. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115182 Canada
CitationJournal: J.Bacteriol. / Year: 2024
Title: Prevalence of Slam-dependent hemophilins in Gram-negative bacteria.
Authors: Shin, H.E. / Pan, C. / Curran, D.M. / Bateman, T.J. / Chong, D.H.Y. / Ng, D. / Shah, M. / Moraes, T.F.
History
DepositionMar 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1263
Polymers27,4721
Non-polymers6542
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.402, 50.313, 125.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemophilin


Mass: 27471.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Microseeding using seed stock obtained from 2.4 M sodium malonate pH 7.0 into final hit condition: 0.1M Tris-HCl pH 8.52 and 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979328 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979328 Å / Relative weight: 1
ReflectionResolution: 1.937→39.3 Å / Num. obs: 24073 / % possible obs: 99.81 % / Redundancy: 11.3 % / CC1/2: 0.998 / Net I/σ(I): 12.23
Reflection shellResolution: 1.937→2.006 Å / Num. unique obs: 2366 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
autoPROCdata processing
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHENIXphasing
PHENIX1.19.2-4158refinement
autoPROCdata reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.937→39.3 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1277 5.31 %
Rwork0.183 --
obs0.1856 24037 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.937→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 44 147 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162018
X-RAY DIFFRACTIONf_angle_d1.5632732
X-RAY DIFFRACTIONf_dihedral_angle_d13.5621208
X-RAY DIFFRACTIONf_chiral_restr0.072293
X-RAY DIFFRACTIONf_plane_restr0.009349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9372-2.01480.33951720.28132450X-RAY DIFFRACTION100
2.0148-2.10650.30811200.23972482X-RAY DIFFRACTION100
2.1065-2.21750.29011480.20732497X-RAY DIFFRACTION100
2.2175-2.35650.25191260.19462508X-RAY DIFFRACTION100
2.3565-2.53840.22051590.18252466X-RAY DIFFRACTION100
2.5384-2.79380.2661210.18682551X-RAY DIFFRACTION100
2.7938-3.1980.23931310.18562538X-RAY DIFFRACTION100
3.198-4.02880.19271630.15742545X-RAY DIFFRACTION100
4.0288-39.30.2121370.17072723X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 36.4487 Å / Origin y: 24.9067 Å / Origin z: 44.4421 Å
111213212223313233
T0.21 Å2-0.0058 Å20.0257 Å2-0.1836 Å2-0.0046 Å2--0.2042 Å2
L3.4974 °2-0.001 °2-0.0183 °2-1.0501 °2-0.2184 °2--0.7734 °2
S0.0647 Å °-0.0781 Å °0.0541 Å °0.056 Å °0.021 Å °0.0638 Å °-0.067 Å °-0.031 Å °-0.1036 Å °
Refinement TLS groupSelection details: all

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