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- PDB-5jt4: L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans: ... -

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Basic information

Entry
Database: PDB / ID: 5jt4
TitleL16A mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state
ComponentsCytochrome c'
KeywordsELECTRON TRANSPORT / gas sensor / cytochrome / nitric oxide
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ASCORBIC ACID / HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKekilli, D. / Strange, R.W. / Hough, M.A.
CitationJournal: Chem Sci / Year: 2017
Title: Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design.
Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N. ...Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N.S. / Andrew, C.R. / Hough, M.A.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Advisory / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
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 2.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,2224
Polymers13,3311
Non-polymers8913
Water3,801211
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4438
Polymers26,6622
Non-polymers1,7816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5030 Å2
ΔGint-43 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.532, 53.532, 180.938
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-483-

HOH

31A-498-

HOH

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Components

#1: Protein Cytochrome c'


Mass: 13331.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2M Ammonium sulfate 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→44.88 Å / Num. obs: 42926 / % possible obs: 98.9 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 22.8
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.3 / % possible all: 95.9

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
SHELXL97refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yli

2yli


Resolution: 1.25→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 --RANDOM
Rwork0.1491 ---
obs-38384 98.9 %-
Displacement parametersBiso max: 76.69 Å2 / Biso mean: 20.9705 Å2 / Biso min: 10.86 Å2
Refinement stepCycle: final / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 60 213 1210
Biso mean--15.76 33.47 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d299
X-RAY DIFFRACTIONs_similar_dist117
X-RAY DIFFRACTIONs_from_restr_planes0.004
X-RAY DIFFRACTIONs_zero_chiral_vol39
X-RAY DIFFRACTIONs_non_zero_chiral_vol4
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.121

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