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- PDB-3ztz: Cytochrome c prime from alcaligenes xylosoxidans: carbon monooxid... -

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Basic information

Entry
Database: PDB / ID: 3ztz
TitleCytochrome c prime from alcaligenes xylosoxidans: carbon monooxide bound L16G variant at 1.05 A resolution: unrestraint refinement
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / HEME C / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsAntonyuk, S.V. / Rustage, N. / Eady, R.R. / Hasnain, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Carbon Monoxide Poisoning is Prevented by the Energy Costs of Conformational Changes in Gas- Binding Haemproteins.
Authors: Antonyuk, S.V. / Rustage, N. / Petersen, C.A. / Arnst, J.L. / Heyes, D.J. / Sharma, R. / Berry, N.G. / Scrutton, N.S. / Eady, R.R. / Andrew, C.R. / Hasnain, S.S.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Data collection
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2223
Polymers13,5751
Non-polymers6472
Water4,936274
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4446
Polymers27,1512
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area3900 Å2
ΔGint-53.7 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.506, 53.506, 181.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CYTOCHROME C'


Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 16 TO GLY
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: 2.76 Å3/Da / Density % sol: 55.49 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULPHATE, HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 4, 2009 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 74665 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2YLG

2ylg


Resolution: 1.05→10 Å / Num. parameters: 13792 / Num. restraintsaints: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: AT THE LAST RUN OF REFINEMENT R-FREE FLAGS WERE REMOVED AND DATA WERE REFINED AGAINST ALL DATA.
RfactorNum. reflection% reflectionSelection details
all0.1629 72483 --
obs--99.5 %-
Rfree---RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 80 / Occupancy sum hydrogen: 877.54 / Occupancy sum non hydrogen: 1219.9
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 45 274 1255

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