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- PDB-6r6m: Kusta0087/Kusta0088 Complex purified from Kuenenia stuttgartiensis -

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Basic information

Entry
Database: PDB / ID: 6r6m
TitleKusta0087/Kusta0088 Complex purified from Kuenenia stuttgartiensis
Components
  • Kusta0088
  • Small soluble cyt c
KeywordsELECTRON TRANSPORT / Heme-c / cystein ligation
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class II / Cytochrome C' / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c/b562 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Class I small soluble cyt c / Small soluble cyt c
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsAkram, M. / Barends, T.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A nitric oxide-binding heterodimeric cytochromeccomplex from the anammox bacteriumKuenenia stuttgartiensisbinds to hydrazine synthase.
Authors: Akram, M. / Reimann, J. / Dietl, A. / Menzel, A. / Versantvoort, W. / Kartal, B. / Jetten, M.S.M. / Barends, T.R.M.
History
DepositionMar 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small soluble cyt c
B: Kusta0088
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4304
Polymers23,1932
Non-polymers1,2372
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.300, 130.360, 45.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein Small soluble cyt c


Mass: 12332.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1Q7P4
#2: Protein Kusta0088


Mass: 10861.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1Q7P3
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20-25% PEG3000, 0.1 M Na-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→63 Å / Num. obs: 29424 / % possible obs: 98.8 % / Redundancy: 6.3 % / Rrim(I) all: 0.06 / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4287 / Rrim(I) all: 0.61 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→45.37 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.26 / Details: TLS (one TLS group per chain)
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1450 4.93 %RANDOM
Rwork0.1884 ---
obs0.1895 29399 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 86 192 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011767
X-RAY DIFFRACTIONf_angle_d0.9722405
X-RAY DIFFRACTIONf_dihedral_angle_d6.5121410
X-RAY DIFFRACTIONf_chiral_restr0.045246
X-RAY DIFFRACTIONf_plane_restr0.005307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.76070.3451260.30922514X-RAY DIFFRACTION90
1.7607-1.83120.30041410.2892734X-RAY DIFFRACTION99
1.8312-1.91450.29091320.22942791X-RAY DIFFRACTION100
1.9145-2.01550.22321320.20652787X-RAY DIFFRACTION100
2.0155-2.14180.22531460.19872788X-RAY DIFFRACTION100
2.1418-2.30710.22071500.19352809X-RAY DIFFRACTION100
2.3071-2.53930.25481510.19982817X-RAY DIFFRACTION100
2.5393-2.90670.21471650.19122809X-RAY DIFFRACTION100
2.9067-3.66180.22281470.17842871X-RAY DIFFRACTION100
3.6618-45.38610.15151600.15843029X-RAY DIFFRACTION100
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)
11.0267-0.15660.58010.61940.06920.96670.059-0.1316-0.48270.31970.10470.47360.0691-0.04330.45930.19280.02070.10580.15870.06980.32229.46328.6291-3.3603
20.2019-0.0206-0.0340.1972-0.23630.4332-0.00490.10110.02440.145-0.00990.0277-0.08630.08240.0060.1598-0.00450.00060.18590.01230.103815.96229.454-14.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 26:200)
2X-RAY DIFFRACTION2(chain B and resseq 27:200)

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