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- PDB-28pb: Crystal structure of CbcA periplasmic domain from Geobacter sulfu... -

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Basic information

Entry
Database: PDB / ID: 28pb
TitleCrystal structure of CbcA periplasmic domain from Geobacter sulfurreducens
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / seven-heme cytochrome / quinol:cytochrome c oxidoreductase / CbcBA complex / Geobacter
Function / homology: / Doubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / oxidoreductase activity / HEME C / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsAntunes, J.M.A. / Correia, M.A.S. / Santos-Silva, T. / Morgado, L.
Funding support Portugal, 6items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia2022.11900.BD Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0140/2020 Portugal
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/4967/2020 Portugal
Fundacao para a Ciencia e a TecnologiaEXPL/BIA-BQM/0770/2021 Portugal
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Bridging inner membrane and periplasm in Geobacter sulfurreducens: structural and biochemical insights into CbcA and its redox partners.
Authors: Antunes, J.M.A. / Silva, M.A. / Correia, M.A.S. / Salgueiro, C.A. / Santos-Silva, T. / Morgado, L.
History
DepositionFeb 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 10, 2026Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97619
Polymers61,2132
Non-polymers8,76417
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-337 kcal/mol
Surface area27180 Å2
Unit cell
Length a, b, c (Å)69.436, 94.167, 114.175
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c


Mass: 30606.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Gene: GSU0594 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74FL3
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.4 M trisodium citrate and 0.1 M sodium HEPES (pH 8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.91→94.17 Å / Num. obs: 58831 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.056 / Rrim(I) all: 0.207 / Net I/σ(I): 9
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 14.2 % / Num. unique obs: 2906 / CC1/2: 0.308 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→72.752 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.601 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.15 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2531 2876 4.894 %
Rwork0.1991 55884 -
all0.202 --
obs-58760 99.985 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.253 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3---0.684 Å2
Refinement stepCycle: LAST / Resolution: 1.91→72.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 605 316 5177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135121
X-RAY DIFFRACTIONr_angle_refined_deg2.1772.0397159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.0055140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9610687
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.18610191
X-RAY DIFFRACTIONr_chiral_restr0.1130.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224182
X-RAY DIFFRACTIONr_nbd_refined0.2260.22223
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2311
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.26
X-RAY DIFFRACTIONr_mcbond_it3.6324.1922218
X-RAY DIFFRACTIONr_mcangle_it5.6687.5072770
X-RAY DIFFRACTIONr_scbond_it4.4124.1842903
X-RAY DIFFRACTIONr_scangle_it6.6867.494387
X-RAY DIFFRACTIONr_lrange_it9.53943.2587948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.91-1.960.3892080.37140500.37242620.8750.88199.90610.37
1.96-2.0130.362110.36939650.36941800.90.88799.90430.368
2.013-2.0720.3222150.32838700.32840860.90.90599.97550.328
2.072-2.1350.3412080.31137500.31239580.9060.9191000.308
2.135-2.2050.3081810.28936770.2938580.9330.9311000.281
2.205-2.2830.2781750.26735230.26736980.9410.9431000.258
2.283-2.3690.3071930.25633930.25935860.9320.9511000.238
2.369-2.4650.2641570.22932950.23134520.950.9631000.208
2.465-2.5750.2721610.20731690.2133300.9490.9711000.182
2.575-2.7010.2541360.19430400.19631760.9620.9761000.169
2.701-2.8460.2871440.19428900.19930340.9470.9751000.164
2.846-3.0190.2281380.19527470.19628850.9630.9761000.167
3.019-3.2270.2361280.17825670.18126950.9630.9811000.156
3.227-3.4850.2481230.19524160.19725390.9620.9781000.173
3.485-3.8160.2551090.18422340.18823430.9630.981000.167
3.816-4.2650.2061210.16719970.16921180.9720.9831000.152
4.265-4.9230.2051150.14117890.14419040.9730.9881000.13
4.923-6.0220.212700.1415370.14316070.9770.9881000.128
6.022-8.4870.262480.15312440.15612920.9650.9891000.145
8.487-72.7520.27350.2147310.2177660.9630.9691000.211
Refinement TLS params.

Method: refined / 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)
10.5528-0.1431-0.05960.28140.13640.16450.0019-0.00310.0559-0.0283-0.01790.00350.03710.00690.0160.0739-0.00150.00450.00790.01160.119428.854912.838513.6983
20.38090.24310.35990.52210.24380.38350.0426-0.0182-0.0280.172-0.01550.02750.081-0.0321-0.02720.136-0.0340.04860.014-0.02020.110220.383813.818536.0403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp5 - 307
2X-RAY DIFFRACTION2ALLBp4 - 307

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