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- PDB-8q1v: TtX183A - A c-type cytochrome domain from the Teredinibacter turn... -

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Basic information

Entry
Database: PDB / ID: 8q1v
TitleTtX183A - A c-type cytochrome domain from the Teredinibacter turnerae protein TERTU_2913
ComponentsPutative lipoprotein
KeywordsELECTRON TRANSPORT / Cytochrome / redox / X183 / CAZy
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) ...: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / Putative lipoprotein
Similarity search - Component
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsRajagopal, B.S. / Hemsworth, G.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N019970/1 United Kingdom
CitationJournal: Iucrj / Year: 2024
Title: Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae.
Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / ...Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / Parkin, A. / Hemsworth, G.R.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6265
Polymers9,9011
Non-polymers7254
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-42 kcal/mol
Surface area4750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.669, 92.669, 92.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Putative lipoprotein


Mass: 9901.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (bacteria) / Gene: TERTU_2913 / Production host: Escherichia coli (E. coli) / References: UniProt: C5BNC6
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20-25 % (w/v) PEG 6000, 1 M LiCl2 and 0.1 M Citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.4→65.53 Å / Num. obs: 27430 / % possible obs: 100 % / Redundancy: 36.9 % / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.029 / Rrim(I) all: 0.129 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-65.5330.60.03623210.0080.037
1.4-1.4237.53.87413260.6290.8943.976

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
Aimlessdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.4→65.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.504 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.193 1355 4.954 %
Rwork0.1645 25996 -
all0.166 --
obs-27351 99.923 %
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: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→65.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 46 60 667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.012647
X-RAY DIFFRACTIONr_bond_other_d0.0010.015554
X-RAY DIFFRACTIONr_angle_refined_deg2.5431.774894
X-RAY DIFFRACTIONr_angle_other_deg0.8061.6291293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.33751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2411091
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7181025
X-RAY DIFFRACTIONr_chiral_restr0.0810.286
X-RAY DIFFRACTIONr_chiral_restr_other0.0340.21
X-RAY DIFFRACTIONr_gen_planes_refined0.030.02777
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02131
X-RAY DIFFRACTIONr_nbd_refined0.350.2151
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2509
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2306
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.27
X-RAY DIFFRACTIONr_nbd_other0.1960.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0790.212
X-RAY DIFFRACTIONr_mcbond_it4.4691.814323
X-RAY DIFFRACTIONr_mcbond_other4.391.811323
X-RAY DIFFRACTIONr_mcangle_it6.883.251404
X-RAY DIFFRACTIONr_mcangle_other6.8953.258405
X-RAY DIFFRACTIONr_scbond_it5.4571.92324
X-RAY DIFFRACTIONr_scbond_other5.4421.919322
X-RAY DIFFRACTIONr_scangle_it8.0163.463486
X-RAY DIFFRACTIONr_scangle_other8.0083.462486
X-RAY DIFFRACTIONr_lrange_it12.7718.24786
X-RAY DIFFRACTIONr_lrange_other11.93217.98777
X-RAY DIFFRACTIONr_rigid_bond_restr3.03231201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4370.264940.2511893X-RAY DIFFRACTION99.8493
1.437-1.4760.271060.2271810X-RAY DIFFRACTION99.8957
1.476-1.5190.211920.1971789X-RAY DIFFRACTION99.8938
1.519-1.5660.187790.1851749X-RAY DIFFRACTION99.8907
1.566-1.6170.185980.1651668X-RAY DIFFRACTION99.774
1.617-1.6740.214920.1691607X-RAY DIFFRACTION99.8824
1.674-1.7370.142640.1521601X-RAY DIFFRACTION99.88
1.737-1.8080.185830.1381518X-RAY DIFFRACTION99.813
1.808-1.8880.138920.1271453X-RAY DIFFRACTION100
1.888-1.980.172750.1281400X-RAY DIFFRACTION100
1.98-2.0870.121670.1321344X-RAY DIFFRACTION100
2.087-2.2130.159610.1421284X-RAY DIFFRACTION99.9257
2.213-2.3660.182580.1431200X-RAY DIFFRACTION100
2.366-2.5550.189640.1421120X-RAY DIFFRACTION100
2.555-2.7990.201530.1511055X-RAY DIFFRACTION100
2.799-3.1280.173380.157960X-RAY DIFFRACTION100
3.128-3.6110.178410.165856X-RAY DIFFRACTION100
3.611-4.4190.2430.163735X-RAY DIFFRACTION100
4.419-6.2360.256300.217592X-RAY DIFFRACTION100
6.236-65.530.275250.243362X-RAY DIFFRACTION100

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