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- PDB-8uf3: Structure of cytochrome c4 from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 8uf3
TitleStructure of cytochrome c4 from Neisseria gonorrhoeae
ComponentsCytochrome C4
KeywordsELECTRON TRANSPORT / Electron transfer / Cytochrome c family
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c4-like / Cytochrome c, class IC / : / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Putative cytochrome
Similarity search - Component
Biological speciesNeisseria gonorrhoeae F62 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhong, F. / Ragusa, M.J. / Pletneva, E.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098502 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128663 United States
CitationJournal: J.Inorg.Biochem. / Year: 2024
Title: The structure of the diheme cytochrome c 4 from Neisseria gonorrhoeae reveals multiple contributors to tuning reduction potentials.
Authors: Zhong, F. / Reik, M.E. / Ragusa, M.J. / Pletneva, E.V.
History
DepositionOct 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome C4
B: Cytochrome C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5459
Polymers40,7822
Non-polymers2,7627
Water93752
1
A: Cytochrome C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7244
Polymers20,3911
Non-polymers1,3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8205
Polymers20,3911
Non-polymers1,4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.047, 168.047, 168.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Cytochrome C4


Mass: 20391.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae F62 (bacteria) / Gene: NGK_0144 / Production host: Escherichia coli (E. coli) / References: UniProt: B4RQ30
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.2 M magnesium sulfate, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.45→39.61 Å / Num. obs: 29063 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 48.19 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.068 / Rrim(I) all: 0.312 / Net I/σ(I): 7.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 22 % / Num. unique obs: 2875 / CC1/2: 0.536 / Rpim(I) all: 0.654 / Rrim(I) all: 3.074 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1-4487-000refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6Q2U

6q2u


Resolution: 2.45→39.61 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 1434 4.93 %
Rwork0.2037 27629 -
obs0.2056 29063 99.92 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.35 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 187 52 2958
Refine LS restraintsType: Distance / Number: 4
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.540.38951100.30092765X-RAY DIFFRACTION99.79
2.54-2.640.3511600.29562715X-RAY DIFFRACTION99.93
2.64-2.760.27541630.26992724X-RAY DIFFRACTION99.9
2.76-2.90.2951660.26422718X-RAY DIFFRACTION100
2.91-3.090.31781660.25382732X-RAY DIFFRACTION100
3.09-3.320.25211400.2542733X-RAY DIFFRACTION100
3.33-3.660.2361510.19152768X-RAY DIFFRACTION100
3.66-4.190.22521330.17322776X-RAY DIFFRACTION100
4.19-5.270.19991230.15952809X-RAY DIFFRACTION100
5.28-39.610.1881220.17442889X-RAY DIFFRACTION99.64

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