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- PDB-9dhe: The crystal structure on the heme/hemoglobin transporter ChuA, in... -

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Basic information

Entry
Database: PDB / ID: 9dhe
TitleThe crystal structure on the heme/hemoglobin transporter ChuA, in complex with heme
ComponentsTonB-dependent receptor
KeywordsTRANSPORT PROTEIN / TonB-dependent transporter / ChuA / Heme / Hemoglobin / Outer-membrane
Function / homology
Function and homology information


heme transmembrane transporter activity / siderophore uptake 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 box, conserved site / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain ...TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemin TonB-dependent receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFox, D. / Grinter, R.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1197376 Australia
Australian Research Council (ARC)LE200100045, LE120100090 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins
Authors: Fox, D.R. / Asadollahi, K. / Samuels, I. / Spicer, B.A. / Kropp, A. / Lupton, C.J. / Lim, K. / Wang, C. / Venugopal, H. / Dramicanin, M. / Knott, G.J. / Grinter, R.
History
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB-dependent receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1752
Polymers69,5581
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 116.112, 123.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein TonB-dependent receptor / Ligand-gated channel protein / TonB-dependent heme/hemoglobin receptor ChuA/ShuA / TonB-dependent ...Ligand-gated channel protein / TonB-dependent heme/hemoglobin receptor ChuA/ShuA / TonB-dependent hemoglobin/transferrin/lactoferrin family receptor


Mass: 69558.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CTF073
Gene: chuA, shuA, B6R15_003762, BE932_16525, D4N09_20470, D9E49_06195, DNX30_14835, EIA08_11240, EPS76_04355, EWK56_15360, ExPECSC038_04966, F7F11_22070, FPI65_21585, G5603_10405, GFY48_03270, GP711_ ...Gene: chuA, shuA, B6R15_003762, BE932_16525, D4N09_20470, D9E49_06195, DNX30_14835, EIA08_11240, EPS76_04355, EWK56_15360, ExPECSC038_04966, F7F11_22070, FPI65_21585, G5603_10405, GFY48_03270, GP711_16795, GQN34_12665, GRC73_08695, HEP34_004102, HI055_004051, HIE29_002171, HL601_09740, HVV39_10295, HVW04_16595, NCTC8621_00323, OGM49_23355
Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: A0A023L3G7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20 % PEG 1500, 0.1 M MIB Buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→48.43 Å / Num. obs: 28374 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 88.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.065 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 3.67 / Num. unique obs: 4040 / CC1/2: 0.442 / Rpim(I) all: 1.286

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.41 Å / SU ML: 0.4781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2992 967 5.06 %
Rwork0.2506 18131 -
obs0.253 19098 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.19 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 43 0 4825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274940
X-RAY DIFFRACTIONf_angle_d0.6476723
X-RAY DIFFRACTIONf_chiral_restr0.046709
X-RAY DIFFRACTIONf_plane_restr0.0053884
X-RAY DIFFRACTIONf_dihedral_angle_d7.1881684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.33931580.29732509X-RAY DIFFRACTION99.74
3.37-3.580.30361220.25792557X-RAY DIFFRACTION99.78
3.58-3.860.32981380.2462564X-RAY DIFFRACTION99.93
3.86-4.240.28541350.22172576X-RAY DIFFRACTION99.89
4.24-4.860.25531340.19552578X-RAY DIFFRACTION99.96
4.86-6.120.27271520.23392599X-RAY DIFFRACTION100
6.12-48.410.32821280.29362748X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 2.3723709092 Å / Origin y: -21.227887992 Å / Origin z: -18.9944875714 Å
111213212223313233
T0.708706497794 Å2-0.0404222924407 Å2-0.0127302102609 Å2-0.79960534975 Å2-0.0762673240468 Å2--0.658370543077 Å2
L1.03786951608 °2-0.50244120616 °2-0.0844374391203 °2-2.70022472452 °2-0.513744176042 °2--1.70219966695 °2
S0.0853595397759 Å °-0.135335773295 Å °-0.028740287754 Å °-0.240271477357 Å °0.085017929857 Å °0.0854592307027 Å °0.0626647449635 Å °0.0825113752134 Å °-0.182278027339 Å °
Refinement TLS groupSelection details: all

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