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- PDB-6hr0: Optimizing electroactive organisms: the effect of orthologous proteins -

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Basic information

Entry
Database: PDB / ID: 6hr0
TitleOptimizing electroactive organisms: the effect of orthologous proteins
ComponentsCytochrome C
KeywordsELECTRON TRANSPORT / extracellular electron transfer / Shewanella / small tetraheme cytochrome / microbial fuel cells / methyl orange / ortholog proteins
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Tetrahaem cytochrome domain / Cytochrome c3 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / PHOSPHITE ION / Cytochrome c
Similarity search - Component
Biological speciesShewanella algae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsTrindade, I.B. / Moe, E. / Matias, P.
Funding support Portugal, 7items
OrganizationGrant numberCountry
Other governmentPTDC/BBB-BQB/4178/2014 Portugal
Other governmentPTDC/BBB-BQB/3554/2014 Portugal
Other governmentERA-MBT/0003/2014 Portugal
Other governmentSFRH/BPD/96952/2013 Portugal
Other governmentSFRH/BPD/93164/2013 Portugal
Other governmentSFRH/BPD/93164/2013 Portugal
Other governmentPD/BD/135187/2017 Portugal
CitationJournal: Frontiers in Energy Research / Year: 2019
Title: Optimizing electroactive organisms: the effect of orthologous proteins
Authors: Fonseca, B.M. / Silva, L. / Trindade, I.B. / Moe, E. / Matias, P.M. / Louro, R.O. / Paquete, C.M.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1466
Polymers9,5931
Non-polymers2,5535
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-77 kcal/mol
Surface area5800 Å2
Unit cell
Length a, b, c (Å)66.171, 66.171, 43.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytochrome C


Mass: 9593.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella algae (bacteria) / Gene: EEY24_16120 / Production host: Shewanella algae (bacteria) / References: UniProt: A0A2T3H499
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bicine pH 8.5 and 3.7 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.04→26.27 Å / Num. obs: 44836 / % possible obs: 96.1 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 14.2
Reflection shellResolution: 1.04→1.07 Å / Num. unique obs: 2412 / CC1/2: 0.386

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1P

1m1p


Resolution: 1.04→26.27 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1778 --
Rwork0.1525 --
obs-44915 99.9 %
Refinement stepCycle: LAST / Resolution: 1.04→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 176 161 998

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