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- PDB-3fpv: Crystal Structure of HbpS -

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Basic information

Entry
Database: PDB / ID: 3fpv
TitleCrystal Structure of HbpS
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
: / Extracellular haem-binding protein
Similarity search - Component
Biological speciesStreptomyces reticuli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.3Mar 20, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular haem-binding protein
B: Extracellular haem-binding protein
C: Extracellular haem-binding protein
D: Extracellular haem-binding protein
E: Extracellular haem-binding protein
F: Extracellular haem-binding protein
G: Extracellular haem-binding protein
H: Extracellular haem-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,81716
Polymers151,3708
Non-polymers4478
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25340 Å2
ΔGint-195 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.522, 152.522, 152.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 3 / Auth seq-ID: 16 - 154 / Label seq-ID: 52 - 190

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
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.: 8
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 / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9778 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2007
RadiationMonochromator: Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 60060 / Num. obs: 59161 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.18 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.63
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.56 / Num. unique all: 12979 / % possible all: 94.9

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Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: Br Phases

Resolution: 2.2→19.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.24 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.285 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26429 2915 5 %RANDOM
Rwork0.20149 ---
all0.20461 60060 --
obs0.20461 55408 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.795 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7976 0 8 513 8497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0228096
X-RAY DIFFRACTIONr_angle_refined_deg0.3581.96411024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg35.22551120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75423.514296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.632151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1641564
X-RAY DIFFRACTIONr_chiral_restr0.0210.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.026192
X-RAY DIFFRACTIONr_nbd_refined0.1830.34275
X-RAY DIFFRACTIONr_nbtor_refined0.3020.55649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5839
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.515
X-RAY DIFFRACTIONr_mcbond_it0.1311.55608
X-RAY DIFFRACTIONr_mcangle_it0.23928752
X-RAY DIFFRACTIONr_scbond_it0.23532656
X-RAY DIFFRACTIONr_scangle_it0.4464.52272
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A556tight positional0.120.5
2B556tight positional0.110.5
3C556tight positional0.130.5
4D556tight positional0.130.5
5E556tight positional0.150.5
6F556tight positional0.180.5
7G556tight positional0.120.5
8H556tight positional0.130.5
1A426loose positional0.4510
2B426loose positional0.3510
3C426loose positional0.4510
4D426loose positional0.4910
5E426loose positional0.510
6F426loose positional0.5710
7G426loose positional0.4710
8H426loose positional0.3810
1A556tight thermal0.510
2B556tight thermal0.6210
3C556tight thermal0.4410
4D556tight thermal0.4810
5E556tight thermal2.4710
6F556tight thermal0.8710
7G556tight thermal0.6110
8H556tight thermal1.6110
1A426loose thermal0.6750
2B426loose thermal0.7750
3C426loose thermal0.5450
4D426loose thermal0.6350
5E426loose thermal2.5850
6F426loose thermal0.9350
7G426loose thermal0.7350
8H426loose thermal1.7850
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 146 -
Rwork0.377 2780 -
obs--89.29 %

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