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- PDB-6tp9: c-type cytochrome NirC -

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Basic information

Entry
Database: PDB / ID: 6tp9
Titlec-type cytochrome NirC
ComponentsCytochrome c55X
KeywordsELECTRON TRANSPORT / cytochrome / 3D domain swapping / heme d1 biosynthesis
Function / homology
Function and homology information


electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c55X
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsKluenemann, T. / Henke, S. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2223/1 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The crystal structure of the heme d1biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo.
Authors: Klunemann, T. / Henke, S. / Blankenfeldt, W.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c55X
B: Cytochrome c55X
C: Cytochrome c55X
D: Cytochrome c55X
E: Cytochrome c55X
F: Cytochrome c55X
G: Cytochrome c55X
H: Cytochrome c55X
J: Cytochrome c55X
K: Cytochrome c55X
I: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,69422
Polymers107,89011
Non-polymers6,80411
Water2,774154
1
A: Cytochrome c55X
C: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8534
Polymers19,6162
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-76 kcal/mol
Surface area8660 Å2
MethodPISA
2
B: Cytochrome c55X
F: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8534
Polymers19,6162
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-78 kcal/mol
Surface area8550 Å2
MethodPISA
3
D: Cytochrome c55X
J: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8534
Polymers19,6162
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-81 kcal/mol
Surface area8670 Å2
MethodPISA
4
E: Cytochrome c55X
K: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8534
Polymers19,6162
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-75 kcal/mol
Surface area8990 Å2
MethodPISA
5
G: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4272
Polymers9,8081
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-21 kcal/mol
Surface area4920 Å2
MethodPISA
6
H: Cytochrome c55X
I: Cytochrome c55X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8534
Polymers19,6162
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-74 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.017, 81.366, 198.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cytochrome c55X


Mass: 9808.213 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: nirC, PA0517 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51479
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 15.3%(v/v) Glycerol 100mM MES pH6.3 10.8% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.188→99.16 Å / Num. obs: 35413 / % possible obs: 92.7 % / Redundancy: 13 % / CC1/2: 0.998 / Rpim(I) all: 0.058 / Net I/σ(I): 10.9
Reflection shellResolution: 2.188→2.469 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1772 / CC1/2: 0.61 / Rpim(I) all: 0.416

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXdev-3707refinement
Aimless0.7.4data scaling
STARANISOdata scaling
CRANK2phasing
PDB_EXTRACT3.25data extraction
AutoPROCdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.19→56.31 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.47
RfactorNum. reflection% reflection
Rfree0.2467 1746 4.93 %
Rwork0.2105 --
obs0.2123 35405 53.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.79 Å2 / Biso mean: 35.2689 Å2 / Biso min: 4.65 Å2
Refinement stepCycle: final / Resolution: 2.19→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6879 0 803 154 7836
Biso mean--29.05 29.09 -
Num. residues----924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.250.755690.3885931022
2.25-2.320.3045200.36693073276
2.32-2.410.2916290.303467370213
2.41-2.50.3406440.29971007105119
2.5-2.620.2908710.2831379145027
2.62-2.760.27651170.26731992210939
2.76-2.930.31641240.26322720284452
2.93-3.150.31022320.2524176440880
3.15-3.470.29442710.22755177544899
3.47-3.970.22632940.19452465540100
3.97-5.010.19192510.168853475598100
5.01-56.310.22032840.19955425826100
Refinement TLS params.Method: refined / Origin x: 1.872 Å / Origin y: 8.3386 Å / Origin z: 153.6707 Å
111213212223313233
T0.0212 Å2-0.03 Å20.0179 Å2-0.0252 Å20.0136 Å2--0.0348 Å2
L0.044 °20.0127 °20.0388 °2-0.1623 °20.158 °2--0.2221 °2
S0.0245 Å °-0.0008 Å °-0.0202 Å °0.0268 Å °-0.0251 Å °-0.0041 Å °0.0371 Å °-0.017 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 88
2X-RAY DIFFRACTION1allA101
3X-RAY DIFFRACTION1allB4 - 88
4X-RAY DIFFRACTION1allB101
5X-RAY DIFFRACTION1allC4 - 88
6X-RAY DIFFRACTION1allC101
7X-RAY DIFFRACTION1allD4 - 83
8X-RAY DIFFRACTION1allD101
9X-RAY DIFFRACTION1allE4 - 88
10X-RAY DIFFRACTION1allE101
11X-RAY DIFFRACTION1allF4 - 88
12X-RAY DIFFRACTION1allF101
13X-RAY DIFFRACTION1allG4 - 88
14X-RAY DIFFRACTION1allG101
15X-RAY DIFFRACTION1allH4 - 84
16X-RAY DIFFRACTION1allH101
17X-RAY DIFFRACTION1allJ4 - 88
18X-RAY DIFFRACTION1allJ101
19X-RAY DIFFRACTION1allK4 - 88
20X-RAY DIFFRACTION1allK101
21X-RAY DIFFRACTION1allI4 - 88
22X-RAY DIFFRACTION1allI101
23X-RAY DIFFRACTION1allS1 - 157

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