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- PDB-5vmm: Staphylococcus aureus IsdB bound to human hemoglobin -

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Basic information

Entry
Database: PDB / ID: 5vmm
TitleStaphylococcus aureus IsdB bound to human hemoglobin
Components
  • (Iron-regulated cell wall-anchored protein) x 2
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsTRANSPORT PROTEIN / heme transfer
Function / homology
Function and homology information


heme transmembrane transporter activity / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport ...heme transmembrane transporter activity / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / erythrocyte development / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / Late endosomal microautophagy / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Iron-regulated surface determinant protein IsdB / Immunoglobulin-like - #1850 / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : ...Iron-regulated surface determinant protein IsdB / Immunoglobulin-like - #1850 / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsBowden, C.F. / Chan, A.C. / Murphy, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-49597 Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses reveal key features in Staphylococcus aureus IsdB-associated unfolding of the heme-binding pocket of human hemoglobin.
Authors: Bowden, C.F.M. / Chan, A.C.K. / Li, E.J.W. / Arrieta, A.L. / Eltis, L.D. / Murphy, M.E.P.
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Iron-regulated cell wall-anchored protein
F: Iron-regulated cell wall-anchored protein
H: Iron-regulated cell wall-anchored protein
J: Iron-regulated cell wall-anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,79210
Polymers173,5598
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19190 Å2
ΔGint-120 kcal/mol
Surface area68870 Å2
Unit cell
Length a, b, c (Å)140.815, 209.114, 70.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Protein Iron-regulated cell wall-anchored protein


Mass: 39302.500 Da / Num. of mol.: 2 / Fragment: UNP residues 125-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: isdA_2, SAMEA3448856_00769, SAMEA3448865_00767, SAMEA3448871_00686
Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1K8PKR3, UniProt: Q7A656*PLUS
#4: Protein Iron-regulated cell wall-anchored protein


Mass: 16436.379 Da / Num. of mol.: 2 / Fragment: UNP residues 125-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: isdA_2, SAMEA3448856_00769, SAMEA3448865_00767, SAMEA3448871_00686
Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1K8PKR3, UniProt: Q7A656*PLUS
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.99 Å3/Da / Density % sol: 58.83 % / Mosaicity: 0.761 ° / Mosaicity esd: 0.01 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M malonic acid pH 5.5, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 46535 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 116.52 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Rrim(I) all: 0.127 / Χ2: 1.251 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.6660.8910.6540.3910.9741.147100
3.66-3.736.10.7050.7560.3090.7711.234100
3.73-3.860.6020.7710.2640.6581.138100
3.8-3.886.10.5440.860.2380.5951.146100
3.88-3.9660.5280.8610.2320.5781.20999.9
3.96-4.056.10.440.8930.1920.4811.187100
4.05-4.166.10.3630.9250.1590.3971.2100
4.16-4.276.10.2880.9470.1260.3141.23799.9
4.27-4.396.10.2280.9720.0990.2491.35100
4.39-4.5460.2060.9770.090.2251.29599.9
4.54-4.76.10.1830.980.080.21.273100
4.7-4.8960.160.9840.0710.1751.193100
4.89-5.1160.1510.9860.0660.1651.19199.9
5.11-5.3860.1380.9870.0610.1511.18699.8
5.38-5.7160.140.9860.0610.1531.21899.9
5.71-6.155.90.1390.9870.0610.1521.29699.7
6.15-6.775.90.1170.990.0510.1281.41799.6
6.77-7.755.80.0860.9950.0390.0951.47599.5
7.75-9.755.60.0440.9980.020.0491.23499.3
9.75-505.50.0410.9980.0190.0451.38598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.21 Å49.79 Å
Translation8.21 Å49.79 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DN1, 3RTL, 4IJ2

2dn1

3rtl

4ij2


Resolution: 3.6→49.794 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.11
RfactorNum. reflection% reflection
Rfree0.3023 3719 8.01 %
Rwork0.2516 --
obs0.2556 46499 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.83 Å2 / Biso mean: 111.2765 Å2 / Biso min: 55.99 Å2
Refinement stepCycle: final / Resolution: 3.6→49.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11741 0 86 0 11827
Biso mean--112.59 --
Num. residues----1470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212109
X-RAY DIFFRACTIONf_angle_d0.67916382
X-RAY DIFFRACTIONf_chiral_restr0.0251771
X-RAY DIFFRACTIONf_plane_restr0.0032089
X-RAY DIFFRACTIONf_dihedral_angle_d11.1724483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5966-3.64210.40141320.37781491162395
3.6421-3.690.35171390.354516391778100
3.69-3.74050.37171390.328815791718100
3.7405-3.7940.39661370.341115611698100
3.794-3.85060.33981370.324215981735100
3.8506-3.91070.30671430.324416111754100
3.9107-3.97480.3871400.340415781718100
3.9748-4.04330.36031350.304215641699100
4.0433-4.11680.36591410.293816041745100
4.1168-4.19590.3551410.29715691710100
4.1959-4.28150.29761440.283415891733100
4.2815-4.37460.35251410.278416271768100
4.3746-4.47630.3461350.258815351670100
4.4763-4.58820.30461340.270416141748100
4.5882-4.71210.35721420.262316021744100
4.7121-4.85070.29181300.265915781708100
4.8507-5.00710.29641410.247616011742100
5.0071-5.18590.30561310.248815721703100
5.1859-5.39330.32371410.248516171758100
5.3933-5.63840.3031370.24815701707100
5.6384-5.93520.31461390.261516011740100
5.9352-6.30640.29461410.25241586172799
6.3064-6.79220.27791310.272815481679100
6.7922-7.47370.26321380.26071608174699
7.4737-8.55040.24381390.221815721711100
8.5504-10.75470.21291340.16211572170699
10.7547-49.79870.28341410.19041590173199

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