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- PDB-4mgf: Crystal structure of apo-PhuS, a heme-binding protein from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 4mgf
TitleCrystal structure of apo-PhuS, a heme-binding protein from Pseudomonas aeruginosa
ComponentsHemin degrading factor
KeywordsMETAL TRANSPORT / host-pathogen interactions / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / heme-trafficking protein / heme-degrading enzyme / heme / HemO
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: 2 Å
AuthorsLee, M.J.Y. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural analysis and identification of PhuS as a heme-degrading enzyme from Pseudomonas aeruginosa.
Authors: Lee, M.J. / Schep, D. / McLaughlin, B. / Kaufmann, M. / Jia, Z.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Water9,044502
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)186.500, 186.500, 41.900
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: 39962.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: phuS / Production host: Escherichia coli (E. coli) / References: UniProt: O68880
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.3 M sodium acetate, 0.1 M Tris, 30% PEG 4000, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 49396 / Num. obs: 48884 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.5 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.703 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 2443 5 %Random
Rwork0.2082 ---
obs0.211 48869 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5345 0 0 502 5847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085469
X-RAY DIFFRACTIONf_angle_d1.1597438
X-RAY DIFFRACTIONf_dihedral_angle_d14.7431982
X-RAY DIFFRACTIONf_chiral_restr0.078816
X-RAY DIFFRACTIONf_plane_restr0.006981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04090.34581420.31962681X-RAY DIFFRACTION100
2.0409-2.08520.3351450.29432773X-RAY DIFFRACTION100
2.0852-2.13370.33411410.28112669X-RAY DIFFRACTION100
2.1337-2.18710.34841460.24632768X-RAY DIFFRACTION100
2.1871-2.24620.29971420.24272700X-RAY DIFFRACTION100
2.2462-2.31230.25831430.21392728X-RAY DIFFRACTION100
2.3123-2.3870.30821440.22392721X-RAY DIFFRACTION99
2.387-2.47230.31061440.23272747X-RAY DIFFRACTION99
2.4723-2.57120.30771420.23132715X-RAY DIFFRACTION100
2.5712-2.68820.28941440.23472731X-RAY DIFFRACTION99
2.6882-2.82990.32771440.242731X-RAY DIFFRACTION99
2.8299-3.00720.30081440.23722739X-RAY DIFFRACTION99
3.0072-3.23930.24251450.2132757X-RAY DIFFRACTION99
3.2393-3.56510.27151420.19172694X-RAY DIFFRACTION98
3.5651-4.08060.21731430.17022721X-RAY DIFFRACTION98
4.0806-5.13960.19741460.15742763X-RAY DIFFRACTION98
5.1396-41.71170.2441460.18542788X-RAY DIFFRACTION96

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