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- PDB-3fhh: Crystal structure of the heme/hemoglobin outer membrane transport... -

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Basic information

Entry
Database: PDB / ID: 3fhh
TitleCrystal structure of the heme/hemoglobin outer membrane transporter ShuA from Shigella dysenteriae
ComponentsOuter membrane heme receptor ShuA
KeywordsMEMBRANE PROTEIN / transporter / tonb-dependent transporter / Membrane / Receptor / TonB box
Function / homology
Function and homology information


heme transmembrane transporter activity / cell outer membrane
Similarity search - Function
TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel ...TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
LEAD (II) ION / Outer membrane heme receptor ShuA
Similarity search - Component
Biological speciesShigella dysenteriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsBrillet, K. / Cobessi, D.
CitationJournal: Proteins / Year: 2010
Title: Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: heme binding by an induced fit mechanism.
Authors: Cobessi, D. / Meksem, A. / Brillet, K.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jun 23, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Outer membrane heme receptor ShuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6946
Polymers70,5731
Non-polymers1,1215
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.099, 114.217, 117.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane heme receptor ShuA


Mass: 70573.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF SHUA (UNP RESIDUES 29-352), LINKER (GSHHHHHH), SHUA (UNP RESIDUES 353-660)
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Gene: shuA / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P72412
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FUSION PROTEIN OF SHUA (UNP RESIDUES 29-352), LINKER (GSHHHHHH), SHUA (UNP RESIDUES 353-660)

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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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13-15% PEG 1K, 0.1M MES pH 6.5, 0.1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9788, 0.9791, 0.9793, 0.9752
DetectorDetector: FLAT PANEL / Date: May 15, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97911
30.97931
40.97521
ReflectionResolution: 2.6→19.94 Å / Num. all: 32798 / Num. obs: 32798 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.09 / Net I/σ(I): 16.27
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.68 / Num. unique all: 3433 / Rsym value: 0.448 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.94 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 26.685 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28581 1647 5 %RANDOM
Rwork0.23736 ---
obs0.23978 31105 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---7.95 Å20 Å2
3---7.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 24 45 4825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214881
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9386637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8985617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99224.249233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38115734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.171531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023805
X-RAY DIFFRACTIONr_nbd_refined0.2410.22092
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.22
X-RAY DIFFRACTIONr_mcbond_it0.5871.53071
X-RAY DIFFRACTIONr_mcangle_it1.0624894
X-RAY DIFFRACTIONr_scbond_it1.69232023
X-RAY DIFFRACTIONr_scangle_it2.4134.51743
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 119 -
Rwork0.336 2218 -
obs--99.87 %

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