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- PDB-4rm6: Crystal structure of Hemopexin Binding Protein -

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Basic information

Entry
Database: PDB / ID: 4rm6
TitleCrystal structure of Hemopexin Binding Protein
ComponentsHeme/hemopexin-binding protein
KeywordsPROTEIN BINDING / beta helix / hemopexin binding protein / hemopexin / Heme-hemopexin-binding protein complex / outer membrane
Function / homology: / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Pectin lyase fold / Pectin lyase fold/virulence factor / extracellular region / Heme/hemopexin-binding protein
Function and homology information
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsZambolin, S. / Clantin, B. / Haouz, A. / Villeret, V. / Delepelaire, P.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for haem piracy from host haemopexin by Haemophilus influenzae.
Authors: Zambolin, S. / Clantin, B. / Chami, M. / Hoos, S. / Haouz, A. / Villeret, V. / Delepelaire, P.
History
DepositionOct 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)96,5941
Polymers96,5941
Non-polymers00
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 177.130, 54.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Heme/hemopexin-binding protein / Heme:hemopexin utilization protein A


Mass: 96594.391 Da / Num. of mol.: 1 / Mutation: C876S, C882S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: Rd KW20 / Gene: HI_0264, hxuA / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P44602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir solution: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, 30% w/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2013
RadiationMonochromator: cryogenically cooled monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 131352 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 11.99 Å2
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.55-1.641.4620655196.8
1.64-1.762.1219701198.4
1.76-1.94.218457198.5
1.9-2.087.8917220199
2.08-2.3212.9315644199.2
2.32-2.6818.5813869199

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Processing

Software
NameVersionClassification
SHARPphasing
BUSTER2.10.1refinement
PROTEUM PLUSPLUSdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→23.39 Å / Cor.coef. Fo:Fc: 0.8644 / Cor.coef. Fo:Fc free: 0.8581 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 6015 5.03 %RANDOM
Rwork0.188 ---
all0.1892 119491 --
obs0.1892 119491 98.81 %-
Displacement parametersBiso mean: 35.56 Å2
Baniso -1Baniso -2Baniso -3
1-20.1186 Å20 Å20 Å2
2---11.0626 Å20 Å2
3----9.0559 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 0 737 6763
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112123HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1621902HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2760SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes203HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1804HARMONIC5
X-RAY DIFFRACTIONt_it12123HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.53
X-RAY DIFFRACTIONt_other_torsion13.84
X-RAY DIFFRACTIONt_chiral_improper_torsion837SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13236SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3382 438 5.04 %
Rwork0.3217 8257 -
all0.3226 8695 -
obs--98.81 %
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)
10.05310.14010.18490.95210.74610.734-0.0371-0.00610.0226-0.03360.00850.0588-0.0411-0.02890.0285-0.0121-0.0029-0.0021-0.0313-0.0081-0.024680.1324187.264-26.0758
20.45340.51010.26671.19390.43040.75-0.04920.01960.07-0.13660.02170.1714-0.0389-0.0640.0275-0.03670.0048-0.0341-0.04880.0137-0.044159.7239147.07-61.5761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 413}A2 - 413
2X-RAY DIFFRACTION2{A|414 - 817}A414 - 817

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