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- PDB-7red: Holo Hemophilin from A. baumannii -

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Basic information

Entry
Database: PDB / ID: 7red
TitleHolo Hemophilin from A. baumannii
ComponentsHemophilin
KeywordsMETAL TRANSPORT / Heme Binding / Secreted
Function / homologyOuter membrane protein/outer membrane enzyme PagP, beta-barrel / PROTOPORPHYRIN IX CONTAINING FE / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii NIPH 201 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsBateman, T.J. / Shah, M. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115182 Canada
CitationJournal: Nat Commun / Year: 2021
Title: A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii.
Authors: Bateman, T.J. / Shah, M. / Ho, T.P. / Shin, H.E. / Pan, C. / Harris, G. / Fegan, J.E. / Islam, E.A. / Ahn, S.K. / Hooda, Y. / Gray-Owen, S.D. / Chen, W. / Moraes, T.F.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7452
Polymers25,1281
Non-polymers6161
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.900, 59.550, 63.740
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 Hemophilin


Mass: 25128.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii NIPH 201 (bacteria)
Gene: F922_02812 / Production host: Escherichia coli (E. coli) / References: UniProt: N9GH75
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.15
Details: 100 mM sodium acetate pH 4.15, 3.25 M sodium formate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 19, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.53→38.692 Å / Num. obs: 29892 / % possible obs: 99.99 % / Redundancy: 14.4 % / CC1/2: 1 / Net I/σ(I): 31.93
Reflection shellResolution: 1.53→1.585 Å / Num. unique obs: 2914 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.53→38.692 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 1494 5 %
Rwork0.1476 28396 -
obs0.1486 29890 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.85 Å2 / Biso mean: 12.247 Å2 / Biso min: 4.04 Å2
Refinement stepCycle: final / Resolution: 1.53→38.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 43 250 1978
Biso mean--13.03 23.83 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.53-1.57940.20541330.16552526
1.5794-1.63580.20061340.16132555
1.6358-1.70130.18371340.14962536
1.7013-1.77880.17991340.14372551
1.7788-1.87250.16331350.14982559
1.8725-1.98990.15651340.1472547
1.9899-2.14350.15691350.13522573
2.1435-2.35920.15891360.14542581
2.3592-2.70050.18631360.16092590
2.7005-3.4020.17191390.14872631
3.402-38.6920.14691440.14072747
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.518-3.7473-1.53825.18463.45363.506-0.2001-0.2936-0.47110.30910.1317-0.10960.49020.1830.06230.14920.02370.01320.09780.04050.135439.563924.857940.7389
21.9599-0.6583-0.42311.8432.03182.3379-0.028-0.0017-0.20330.12920.03420.14120.1797-0.0462-0.02970.1229-0.01540.01310.04540.02710.106933.389720.719233.7394
32.66241.13480.66132.3348-0.2523.47810.1128-0.0921-0.07270.1787-0.05240.09970.1396-0.0278-0.04170.0832-0.01340.00590.05-0.00760.068231.768521.469631.3253
41.2017-1.47561.15288.2037-1.74166.36760.04530.1291-0.0233-0.23280.011-0.03470.0259-0.041-0.05540.052-0.02890.00310.0931-0.01680.049931.079229.918219.6652
54.85620.23861.3531.39180.51361.1528-0.08950.30970.16820.00040.04270.0202-0.0066-0.04810.02890.07730.0021-0.00660.0473-0.0080.034934.357633.978624.4502
65.6264-1.216-2.10721.67280.12942.8546-0.03270.1404-0.1054-0.0517-0.00230.00540.11270.02230.04380.0461-0.0087-0.00160.0485-0.00690.031641.058730.444228.4991
75.8767-2.54641.90143.55312.81916.35330.01170.1205-0.0098-0.0226-0.05440.1694-0.001-0.19660.06360.04450.00090.0170.08110.01650.059327.756836.838236.844
81.7295-0.0201-0.00270.6365-0.1180.56220.02240.0844-0.1311-0.0353-0.0349-0.07390.05060.05570.01030.06240.0046-0.00660.06590.00070.04947.155732.31134.0277
92.8606-1.99270.52622.3832-0.40380.6145-0.0084-0.0654-0.02940.08810.0065-0.08670.0010.05920.0110.0503-0.0112-0.01420.07730.02560.077353.586638.556338.6286
101.9544-2.5612-0.37734.41890.88920.9514-0.0104-0.0459-0.01640.1147-0.0247-0.03380.0297-0.04510.03250.0449-0.0116-0.0040.08860.02290.048447.565138.540744.0556
111.3286-0.859-0.10482.42280.59580.666-0.02090.0183-0.02450.0938-0.0272-0.06120.0374-0.00920.04790.0366-0.009-0.01130.04940.01350.038946.989134.837.1499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2(chain A and resid 22:29)A22 - 29
2X-RAY DIFFRACTION3(chain A and resid 30:53)A30 - 53
3X-RAY DIFFRACTION4(chain A and resid 54:65)A54 - 65
4X-RAY DIFFRACTION5(chain A and resid 66:96)A66 - 96
5X-RAY DIFFRACTION6(chain A and resid 97:113)A97 - 113
6X-RAY DIFFRACTION7(chain A and resid 114:121)A114 - 121
7X-RAY DIFFRACTION8(chain A and resid 122:158)A122 - 158
8X-RAY DIFFRACTION9(chain A and resid 159:198)A159 - 198
9X-RAY DIFFRACTION10(chain A and resid 199:223)A199 - 223
10X-RAY DIFFRACTION11(chain A and resid 224:251)A224 - 251

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