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- PDB-5khl: Crystal Structure of periplasmic Heme binding protein HutB of Vib... -

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Basic information

Entry
Database: PDB / ID: 5khl
TitleCrystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae
ComponentsHemin ABC transporter, periplasmic hemin-binding protein HutB
KeywordsTRANSPORT PROTEIN / Hemin / ABC trasporter / periplasmic protein / Vibrio cholerae
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hemin ABC transporter, periplasmic hemin-binding protein HutB
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsAgarwal, S. / Dey, S. / Ghosh, B. / Dasgupta, J.
Funding support India, 1items
OrganizationGrant numberCountry
DAE (BRNS)2013/37B/26/brns India
Citation
Journal: To be published
Title: Crystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae
Authors: Agarwal, S. / Biswas, M. / Dasgupta, J.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae.
Authors: Agarwal, S. / Biswas, M. / Dasgupta, J.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
B: Hemin ABC transporter, periplasmic hemin-binding protein HutB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9572
Polymers28,8611
Non-polymers961
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.884, 62.884, 135.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hemin ABC transporter, periplasmic hemin-binding protein HutB


Mass: 28860.943 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: hutB, VC0395_0324 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AE70
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8 M ammonium sulfate, 0.1 M HEPES (pH 7.0) against a reservoir solution 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.397→37 Å / Num. obs: 11192 / % possible obs: 99.2 % / Redundancy: 9.7 % / Net I/σ(I): 29.9
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata processing
SCALAdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RG7

2rg7


Resolution: 2.397→28.53 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 1115 9.99 %
Rwork0.1995 --
obs0.2051 11157 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 5 48 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091946
X-RAY DIFFRACTIONf_angle_d1.2972647
X-RAY DIFFRACTIONf_dihedral_angle_d17.78734
X-RAY DIFFRACTIONf_chiral_restr0.046323
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.397-2.5060.43511360.31291225X-RAY DIFFRACTION98
2.506-2.6380.33631360.28821225X-RAY DIFFRACTION99
2.638-2.80320.36491380.26441238X-RAY DIFFRACTION99
2.8032-3.01940.30791370.25281236X-RAY DIFFRACTION99
3.0194-3.32280.28341410.21031263X-RAY DIFFRACTION99
3.3228-3.80270.26311380.18821239X-RAY DIFFRACTION99
3.8027-4.78730.20131410.1581276X-RAY DIFFRACTION98
4.7873-28.53250.21891480.18271340X-RAY DIFFRACTION96
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)
10.6684-1.1319-0.50371.66671.36453.9836-0.0734-0.1580.0434-0.39450.0005-0.0597-0.66430.0272-00.449-0.01940.04890.3185-0.03170.398124.68539.033419.4154
21.95581.48460.53442.3040.18550.68960.3744-0.2806-0.3188-0.092-0.2871-0.05490.0392-0.106500.5011-0.03620.01630.4110.05490.416517.8474-16.263911.9502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 22 through 130 )
2X-RAY DIFFRACTION2chain 'B' and (resid 131 through 277 )

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