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- PDB-6zsk: Cytochrome c prime beta from Methylococcus capsulatus (Bath): CO ... -

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Basic information

Entry
Database: PDB / ID: 6zsk
TitleCytochrome c prime beta from Methylococcus capsulatus (Bath): CO complex
ComponentsCytochrome c
KeywordsOXIDOREDUCTASE / cytochrome c'-beta / methanotroph / carbon monoxide
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / CARBON MONOXIDE / HEME C / Cytochrome c
Function and homology information
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAdams, H.R. / Hough, M.A.
CitationJournal: To Be Published
Title: to be published
Authors: Adams, H.R. / Strange, R.W. / Svistunenko, D.A. / Andrew, C.R. / Hough, M.A.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,41511
Polymers34,7412
Non-polymers1,6739
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-111 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.490, 105.490, 105.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

21A-203-

ZN

31A-313-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c


Mass: 17370.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: ccp, MCA2394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD5

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 35% PEG 550 (v/v) and 0.1 M MES, pH 6.5. ...Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 35% PEG 550 (v/v) and 0.1 M MES, pH 6.5. Cryoprotection in ML plus 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→47.22 Å / Num. obs: 51778 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 1 / Rrim(I) all: 0.069 / Net I/σ(I): 26.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2607 / CC1/2: 0.5 / Rrim(I) all: 2.73 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Refined from PDB 6HIH

6hih


Resolution: 1.6→47.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.701 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2626 5.1 %RANDOM
Rwork0.1811 ---
obs0.182 49120 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.19 Å2 / Biso mean: 29.735 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 114 131 2340
Biso mean--33.12 40.91 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181984
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.7513174
X-RAY DIFFRACTIONr_angle_other_deg1.5031.6274578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45121.527131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91815323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9451516
X-RAY DIFFRACTIONr_chiral_restr0.090.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02542
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 177 -
Rwork0.306 3645 -
all-3822 -
obs--100 %

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