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- PDB-7re4: Apo Hemophilin from A. baumannii -

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Basic information

Entry
Database: PDB / ID: 7re4
TitleApo Hemophilin from A. baumannii
ComponentsHemophilin
KeywordsMETAL TRANSPORT / Heme Binding / Secreted
Function / homologyOuter membrane protein/outer membrane enzyme PagP, beta-barrel / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii NIPH 201 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 1.1Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Hemophilin
C: Hemophilin
E: Hemophilin


Theoretical massNumber of molelcules
Total (without water)75,3843
Polymers75,3843
Non-polymers00
Water8,953497
1
A: Hemophilin


Theoretical massNumber of molelcules
Total (without water)25,1281
Polymers25,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Hemophilin


Theoretical massNumber of molelcules
Total (without water)25,1281
Polymers25,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Hemophilin


Theoretical massNumber of molelcules
Total (without water)25,1281
Polymers25,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.110, 145.560, 153.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemophilin


Mass: 25128.086 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100 mM Hepes pH 7, 10% (w/v) PEG 6K

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 19, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.87→39.87 Å / Num. obs: 65838 / % possible obs: 99.97 % / Redundancy: 15 % / CC1/2: 0.995 / Net I/σ(I): 9.93
Reflection shellResolution: 1.87→1.937 Å / Num. unique obs: 6505 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RED

7red


Resolution: 1.87→39.87 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3289 5 %
Rwork0.172 62537 -
obs0.1739 65826 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.08 Å2 / Biso mean: 22.8368 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.87→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 0 497 5508
Biso mean---30.01 -
Num. residues----722
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.89790.33681400.29452659
1.8979-1.92760.32671410.26842709
1.9276-1.95920.26371410.23552675
1.9592-1.9930.26531420.22042699
1.993-2.02920.27191430.22072711
2.0292-2.06820.23081400.19172672
2.0682-2.11040.25571420.19252693
2.1104-2.15630.21061420.18962699
2.1563-2.20650.23681410.18272685
2.2065-2.26170.22861430.18232706
2.2617-2.32280.20071430.18362710
2.3228-2.39110.21111420.18182707
2.3911-2.46830.24711420.18122697
2.4683-2.55650.21471420.1772702
2.5565-2.65890.22571430.18042710
2.6589-2.77980.2351430.17192724
2.7798-2.92640.21611430.16892721
2.9264-3.10960.20791440.16622732
3.1096-3.34960.1891440.16052733
3.3496-3.68650.18561460.15172765
3.6865-4.21940.20361440.14892743
4.2194-5.31410.14161460.12162781
5.3141-39.870.15911520.15842904
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)
12.2841-0.1311-2.13393.4744-1.8963.1978-0.0407-0.0835-0.13380.02570.00750.01460.1302-0.06580.04020.11630.0205-0.02510.1853-0.01490.084213.864-1.60228.18
21.0167-0.4102-0.36230.56970.10070.660.00470.01610.02160.0414-0.01530.0121-0.0031-0.04190.01060.1285-0.011-0.00520.12530.00770.106616.2670.79615.466
33.2820.83262.03945.6482.29514.1481-0.0935-0.63010.40560.67520.0446-0.2113-0.07730.13550.03960.29920.0889-0.03740.4318-0.08360.174521.8787.06762.95
42.2819-0.60170.27510.8788-0.1280.4909-0.0447-0.19170.19280.15280.0231-0.1279-0.01940.01210.02570.14570.002-0.01580.1626-0.0240.109619.0374.67849.781
54.8387-4.73451.49058.924-4.69085.45240.04850.1239-0.4106-0.3164-0.2311-0.06950.79630.19720.0540.3231-0.00720.03640.14640.00010.270311.52427.5250.54
62.4826-0.5314-0.87340.5139-0.06341.7308-0.0178-0.0151-0.028-0.0066-0.0169-0.05150.05360.05940.03620.1370.01050.00170.08820.03220.1658.79940.7134.333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:48 )A22 - 48
2X-RAY DIFFRACTION2( CHAIN A AND RESID 49:251 )A49 - 251
3X-RAY DIFFRACTION3( CHAIN C AND RESID 22:49 )C22 - 49
4X-RAY DIFFRACTION4( CHAIN C AND RESID 50:251 )C50 - 251
5X-RAY DIFFRACTION5( CHAIN E AND RESID 22:47 )E22 - 47
6X-RAY DIFFRACTION6( CHAIN E AND RESID 48:251 )E48 - 251

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