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- PDB-5jli: Nitric oxide complex of the L16A mutant of cytochrome c prime fro... -

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Basic information

Entry
Database: PDB / ID: 5jli
TitleNitric oxide complex of the L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans
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 / NITRIC OXIDE / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionApr 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
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: 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

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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)14,6066
Polymers13,5891
Non-polymers1,0175
Water2,360131
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,21212
Polymers27,1792
Non-polymers2,03410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5700 Å2
ΔGint-119 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.629, 53.629, 180.523
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-428-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cytochrome c'


Mass: 13589.362 Da / Num. of mol.: 1 / Mutation: L16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Plasmid: pET26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00138
#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

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Non-polymers , 4 types, 135 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2 M 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 27, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→46.44 Å / Num. obs: 23047 / % possible obs: 98.8 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yl0

2yl0


Resolution: 1.55→46.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.497 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1155 5 %RANDOM
Rwork0.1705 ---
obs0.1728 21801 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.31 Å2 / Biso mean: 22.068 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.19 Å20 Å2
2---0.37 Å20 Å2
3---1.2 Å2
Refinement stepCycle: final / Resolution: 1.55→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 67 135 1157
Biso mean--21.8 29.95 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021147
X-RAY DIFFRACTIONr_bond_other_d0.0020.021069
X-RAY DIFFRACTIONr_angle_refined_deg2.1842.0631582
X-RAY DIFFRACTIONr_angle_other_deg1.02432480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50624.25547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95415188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.954157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02255
X-RAY DIFFRACTIONr_mcbond_it2.2741.939548
X-RAY DIFFRACTIONr_mcbond_other2.2521.929546
X-RAY DIFFRACTIONr_mcangle_it2.8522.916694
X-RAY DIFFRACTIONr_rigid_bond_restr2.25132215
X-RAY DIFFRACTIONr_sphericity_free27.816523
X-RAY DIFFRACTIONr_sphericity_bonded14.30152289
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 70 -
Rwork0.269 1570 -
all-1640 -
obs--98.14 %

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