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- PDB-9o0k: ChtA CR domain from Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 9o0k
TitleChtA CR domain from Corynebacterium diphtheriae
ComponentsMembrane protein
KeywordsTRANSPORT PROTEIN / CR / Complex
Function / homologyHtaa / Htaa / membrane / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Membrane protein
Function and homology information
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.629 Å
AuthorsFord, J. / Sawaya, M.R. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI161828 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural Basis of Heme Scavenging by the ChtA and HtaA Hemophores in Corynebacterium diphtheriae.
Authors: Ford, J. / Goring, A.K. / Lee, Y. / Chen, M. / Mahoney, B.J. / Sawaya, M.R. / Shafaat, H.S. / Loo, J.A. / Clubb, R.T.
History
DepositionApr 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 17, 2025Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
B: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,09818
Polymers39,6462
Non-polymers2,45216
Water4,035224
1
A: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9508
Polymers19,8231
Non-polymers1,1277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,14810
Polymers19,8231
Non-polymers1,3259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.258, 188.772, 119.176
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Membrane protein


Mass: 19822.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Gene: DIP1520 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NGJ3

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Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.629→19.437 Å / Num. obs: 34917 / % possible obs: 89 % / Redundancy: 11.69 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1216 / Rpim(I) all: 0.0367 / Rrim(I) all: 0.1272 / Net I/σ(I): 10.26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.222-19.43711.710.069124.562042820428174517450.994-0.2990.02110.07240.68499.910099.910099.96.74100
4.118-5.22211.310.075224.861973119731174417440.998-0.2670.0230.07870.66699.899.799.899.799.86.1999.7
3.589-4.11812.30.086224.392143121431174317430.997-0.3540.02540.090.69799.899.899.899.899.86.6699.8
3.253-3.58912.750.098521.092221522215174317430.998-0.3220.02870.10270.68799.899.899.899.899.86.7999.8
3.013-3.25311.970.120716.152089820898174617460.996-0.2230.03680.12630.70899.999.999.999.999.96.3699.9
2.829-3.01312.860.136513.972248322483174817480.997-0.2550.03960.14230.69899.999.999.999.999.96.8199.9
2.685-2.82913.080.169311.852281622816174517450.996-0.2430.04850.17620.711001001001001006.89100
2.567-2.68513.090.21069.842286422864174717470.995-0.0960.06020.21920.72599.999.999.999.999.96.999.9
2.465-2.56712.230.25028.42136621366174717470.992-0.0650.07450.26120.72399.999.999.999.999.96.499.9
2.378-2.46511.610.30196.622025320253174517450.992-0.1690.09250.31610.721001001001001006.06100
2.3-2.37812.240.30496.682137521375174617460.993-0.0480.09050.31830.7497.997.397.997.397.96.3897.3
2.229-2.312.280.31456.392146821468174817480.991-0.0290.09330.32840.6993.293.193.293.193.26.4393.1
2.162-2.22912.590.34176.242196821968174517450.993-0.1440.09980.35630.6958787.38787.3876.6187.3
2.097-2.16212.50.44375.132182321823174617460.986-0.090.13040.46290.68783.984.683.981.981.16.5484.6
2.037-2.09711.330.51734.381978119781174617460.978-0.0410.16060.54230.7458585.88576.576.15.9385.8
1.978-2.03710.920.53964.031908819088174817480.975-0.0290.17180.56720.70884.585.484.570.1695.7185.4
1.92-1.97811.560.6343.72017320173174517450.959-0.0640.19390.66380.71584.685.784.663.261.66.0885.7
1.861-1.9211.630.80433.012031620316174717470.936-0.0440.2450.84190.7178384.28355.553.76.1184.2
1.797-1.86110.510.89032.561837418374174817480.915-0.070.28340.93630.69479.681.379.644.742.25.6381.3
1.629-1.7975.340.99651.5193179317174517450.585-0.0250.45121.10260.72847.447.647.413.112.12.8947.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.629→17.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1742 -RANDOM
Rwork0.2314 ---
obs0.2326 34869 65.5 %-
Displacement parametersBiso mean: 24.84 Å2
Baniso -1Baniso -2Baniso -3
1-3.2232 Å20 Å20 Å2
2---0.9435 Å20 Å2
3----2.2797 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.629→17.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 163 224 3121
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012965HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033989HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1041SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes565HARMONIC5
X-RAY DIFFRACTIONt_it2965HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2517SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion14.96
LS refinement shellResolution: 1.63→1.74 Å
RfactorNum. reflection% reflection
Rfree0.4372 38 -
Rwork0.3259 --
obs0.3316 698 7.29 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5571-1.0487-0.1535.66630.36680.88380.17230.0898-0.02570.0898-0.20590.0206-0.02570.02060.0336-0.00650.0014-0.0575-0.0388-0.0226-0.09722.931617.7677-13.4803
21.13030.5370.14.5652-0.15670.88870.1574-0.0337-0.0323-0.0337-0.182-0.0305-0.0323-0.03050.02460.00080.0002-0.0322-0.02450.0024-0.086115.101527.643813.5062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A115 - 290
2X-RAY DIFFRACTION1{ A|* }A300 - 313
3X-RAY DIFFRACTION2{ B|* }B115 - 291
4X-RAY DIFFRACTION2{ B|* }B300 - 337

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