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- PDB-4imh: Crystal Structure of Cytoplasmic Heme Binding Protein, PhuS, from... -

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Basic information

Entry
Database: PDB / ID: 4imh
TitleCrystal Structure of Cytoplasmic Heme Binding Protein, PhuS, from Pseudomonas aeruginosa
ComponentsHemin degrading factor
KeywordsMETAL TRANSPORT / TRANSPORT PROTEIN / Heme Transport / Heme Oxygenase
Function / homology
Function and homology information


iron ion transport / metal ion binding
Similarity search - Function
Haemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / : / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hemin degrading factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsTripathi, S.M. / Poulos, T.L.
CitationJournal: J.Inorg.Biochem. / Year: 2013
Title: Crystal structure of the Pseudomonas aeruginosa cytoplasmic heme binding protein, Apo-PhuS.
Authors: Tripathi, S. / O'Neill, M.J. / Wilks, A. / Poulos, T.L.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemin degrading factor
B: Hemin degrading factor


Theoretical massNumber of molelcules
Total (without water)79,9242
Polymers79,9242
Non-polymers00
Water6,684371
1
A: Hemin degrading factor


Theoretical massNumber of molelcules
Total (without water)39,9621
Polymers39,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemin degrading factor


Theoretical massNumber of molelcules
Total (without water)39,9621
Polymers39,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.730, 187.730, 42.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Hemin degrading factor


Mass: 39962.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: phuS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: O68880
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M HEPES(7.5), 25% polyacrylic acid 5100, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 1.976→46.93 Å / Num. obs: 51833 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 1.976→2.08 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQ2

2hq2
PDB Unreleased entry


Resolution: 1.976→41.978 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2644 5.1 %
Rwork0.1753 --
obs0.1777 51820 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.976→41.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 0 371 5789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135586
X-RAY DIFFRACTIONf_angle_d1.4527605
X-RAY DIFFRACTIONf_dihedral_angle_d13.9752025
X-RAY DIFFRACTIONf_chiral_restr0.061830
X-RAY DIFFRACTIONf_plane_restr0.0081008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.976-2.01190.2891440.2222602X-RAY DIFFRACTION100
2.0119-2.05060.3151340.20412559X-RAY DIFFRACTION100
2.0506-2.09250.22151480.20052596X-RAY DIFFRACTION100
2.0925-2.1380.27331490.18482608X-RAY DIFFRACTION100
2.138-2.18770.24681630.18252572X-RAY DIFFRACTION100
2.1877-2.24240.22851280.1792625X-RAY DIFFRACTION100
2.2424-2.30310.23911300.16942592X-RAY DIFFRACTION100
2.3031-2.37080.19251370.17062631X-RAY DIFFRACTION100
2.3708-2.44730.22381270.16972571X-RAY DIFFRACTION100
2.4473-2.53480.27621300.18882649X-RAY DIFFRACTION100
2.5348-2.63630.2341370.19582624X-RAY DIFFRACTION100
2.6363-2.75620.28941420.20462585X-RAY DIFFRACTION100
2.7562-2.90150.25391240.20132624X-RAY DIFFRACTION100
2.9015-3.08320.22741340.22641X-RAY DIFFRACTION100
3.0832-3.32120.25791600.1882624X-RAY DIFFRACTION100
3.3212-3.65530.19081510.1652606X-RAY DIFFRACTION100
3.6553-4.18380.18021410.15032647X-RAY DIFFRACTION99
4.1838-5.26950.15891360.1362611X-RAY DIFFRACTION97
5.2695-41.98720.2431290.18562209X-RAY DIFFRACTION80
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)
12.44010.8944-0.31993.6055-0.40390.71170.0922-0.07490.21430.0824-0.0621-0.2024-0.00270.0663-0.02630.17410.00740.01740.2090.00730.128535.3699-0.06222.3618
22.50881.0252-0.53983.5617-0.25531.26850.1575-0.3858-0.35890.4339-0.3411-0.4865-0.04130.23070.13220.30770.0068-0.06680.29650.11440.3863.3385-24.47810.8049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 354 )
2X-RAY DIFFRACTION2chain 'B' and (resid 8 through 354 )

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