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- PDB-3fpw: Crystal Structure of HbpS with bound iron -

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Basic information

Entry
Database: PDB / ID: 3fpw
TitleCrystal Structure of HbpS with bound iron
ComponentsExtracellular haem-binding protein
KeywordsHEME binding protein / haem binding
Function / homology
Function and homology information


: / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Extracellular haem-binding protein
Similarity search - Component
Biological speciesStreptomyces reticuli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOrtiz de Orue Lucana, D. / Bogel, G. / Zou, P. / Groves, M.R.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: The oligomeric assembly of the novel haem-degrading protein HbpS is essential for interaction with its cognate two-component sensor kinase
Authors: Ortiz de Orue Lucana, D. / Bogel, G. / Zou, P. / Groves, M.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary characterization of a novel haem-binding protein of Streptomyces reticuli
Authors: Zou, P. / Groves, M.R. / Viale-Bouroncle, S.D. / Ortiz de Orue Lucana, D.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular haem-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4137
Polymers18,9211
Non-polymers4926
Water2,396133
1
A: Extracellular haem-binding protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)155,30256
Polymers151,3708
Non-polymers3,93348
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area31080 Å2
ΔGint-360 kcal/mol
Surface area36130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.940, 77.940, 79.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-157-

FE

21A-227-

HOH

31A-292-

HOH

DetailsBIOPHYSICAL EXPERIMENTS INDICATE THAT THE IN VITRO SOLUTION STATE IS OCTOMERIC

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Components

#1: Protein Extracellular haem-binding protein / HBPS


Mass: 18921.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces reticuli (bacteria) / Gene: hbpS / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RIM2
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.605033 Å3/Da / Density % sol: 23.36606 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 40% w/v PEG 400, 5% w/v PEG 3000, 100mM MES pH 5.8; Protein concentration of 14 mg/ml and preincubated with haemin, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2007
RadiationMonochromator: Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 16602 / Num. obs: 16582 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 20.23 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.73
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 85.17 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2712 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.4.0077refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPV

3fpv


Resolution: 1.6→18.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.207 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.12 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18911 837 5 %RANDOM
Rwork0.15423 ---
all0.156 16602 --
obs0.156 15744 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 22 133 1175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.88
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.969
X-RAY DIFFRACTIONr_chiral_restr0.089
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_mcbond_it1.011
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 50 -
Rwork0.191 1140 -
obs--100 %

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