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- PDB-2yl3: CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXID... -

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Basic information

Entry
Database: PDB / ID: 2yl3
TitleCYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16G VARIANT AT 1.04 A RESOLUTION - RESTRAINT REFINED
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HAEMOPROTEIN / 4-HELIX BUNDLE
Function / homology
Function and homology information


electron transport chain / electron transfer activity / periplasmic space / 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 / MOLECULAR REPLACEMENT / Resolution: 1.04 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
DepositionMay 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other / Polymer sequence
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_poly / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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)14,3184
Polymers13,5751
Non-polymers7433
Water6,161342
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6368
Polymers27,1512
Non-polymers1,4856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4210 Å2
ΔGint-79.3 kcal/mol
Surface area12730 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
Components on special symmetry positions
IDModelComponents
11A-2055-

HOH

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Components

#1: Protein CYTOCHROME C' / CYTOCHROME C PRIME


Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Plasmid: PEC86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138
#2: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.74 Å3/Da / Density % sol: 55.19 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULPHATE, TRIS PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2010 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 74665 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 11.8 Å2 / 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
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YL0

2yl0


Resolution: 1.04→46.34 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.681 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.14575 3755 5 %RANDOM
Rwork0.12504 ---
obs0.12609 70650 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.807 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.04→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 50 342 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221333
X-RAY DIFFRACTIONr_bond_other_d0.0050.02648
X-RAY DIFFRACTIONr_angle_refined_deg1.7522.0571846
X-RAY DIFFRACTIONr_angle_other_deg0.9413.0031481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72825.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.148157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211431
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02188
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.491.5819
X-RAY DIFFRACTIONr_mcbond_other0.4521.5183
X-RAY DIFFRACTIONr_mcangle_it2.31221314
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1613514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.414.5516
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.23431981
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 260 -
Rwork0.268 5021 -
obs--97.18 %

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