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- PDB-6r6n: Recombinantly produced Kusta0087/Kusta0088 Complex, C32M/C101M mutant -

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Basic information

Entry
Database: PDB / ID: 6r6n
TitleRecombinantly produced Kusta0087/Kusta0088 Complex, C32M/C101M mutant
Components
  • KustA0088
  • Small soluble cyt c
KeywordsELECTRON TRANSPORT / Heme-c / cystein ligation
Function / homology
Function and homology information


electron transport chain / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
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 / FOURIER SYNTHESIS / Resolution: 2 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 1.1Oct 23, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Nov 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
Revision 1.3Jan 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small soluble cyt c
B: KustA0088
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5574
Polymers23,3202
Non-polymers1,2372
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-50 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.680, 130.430, 45.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Small soluble cyt c


Mass: 12431.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: KSMBR1_3082, kusta0087 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1Q7P4
#2: Protein KustA0088


Mass: 10889.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: KSMBR1_3083, kusta0088 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1Q7P3
#3: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.88 %
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, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→63 Å / Num. obs: 18722 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rrim(I) all: 0.123 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.4 % / Num. unique obs: 2465 / Rrim(I) all: 0.736 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6R6M

6r6m


Resolution: 2→45.66 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 960 5.14 %RANDOM
Rwork0.1997 ---
obs0.2016 18665 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 86 129 1827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081764
X-RAY DIFFRACTIONf_angle_d1.0632403
X-RAY DIFFRACTIONf_dihedral_angle_d7.0681404
X-RAY DIFFRACTIONf_chiral_restr0.052247
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.10540.31731430.2732442X-RAY DIFFRACTION99
2.1054-2.23730.28061260.2342489X-RAY DIFFRACTION99
2.2373-2.410.27121300.22742489X-RAY DIFFRACTION99
2.41-2.65250.3511410.23252512X-RAY DIFFRACTION100
2.6525-3.03630.26121430.23912526X-RAY DIFFRACTION100
3.0363-3.82510.21751400.19652552X-RAY DIFFRACTION100
3.8251-45.67190.17541370.15332695X-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)
10.77660.27270.32010.3875-0.21110.5468-0.05540.0661-0.41160.14130.05860.3702-0.05220.0084-0.00010.2380.01820.09080.20260.01860.393954.32188.49719.8182
20.4647-0.1011-0.08940.3652-0.36460.5678-0.00380.03710.06050.0218-0.00450.0562-0.0530.032-00.2156-0.00720.00640.21590.01020.160561.042829.19118.4209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 25 through 135)
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 126)

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