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- PDB-3zwi: RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDA... -

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Basic information

Entry
Database: PDB / ID: 3zwi
TitleRECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A: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
ASCORBIC ACID / CARBON MONOXIDE / HEME C / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsAntonyuk, S. / 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 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
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 2.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 23, 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: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5505
Polymers13,6311
Non-polymers9194
Water4,612256
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,10010
Polymers27,2632
Non-polymers1,8378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area5220 Å2
ΔGint-83.9 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.914, 53.914, 180.864
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2244-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein CYTOCHROME C'


Mass: 13631.442 Da / Num. of mol.: 1
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
#5: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM

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Non-polymers , 4 types, 259 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULPHATE, HEPES BUFFER., pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2008 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→36.9 Å / Num. obs: 40961 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 81.2

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YLD

2yld


Resolution: 1.25→10 Å / Num. parameters: 269 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 2163 5.3 %RANDOM
all0.142 43009 --
obs0.1402 -97.83 %-
Refine analyzeNum. disordered residues: 47 / Occupancy sum hydrogen: 913.5 / Occupancy sum non hydrogen: 1248
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 62 256 1267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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