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- PDB-5js5: Nitric oxide complex of the L16F mutant of cytochrome c prime fro... -

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Basic information

Entry
Database: PDB / ID: 5js5
TitleNitric oxide complex of the L16F 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: 1.7 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 7, 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)14,2324
Polymers13,4071
Non-polymers8253
Water1,838102
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4638
Polymers26,8142
Non-polymers1,6496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4820 Å2
ΔGint-55 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.207, 53.207, 181.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cytochrome c' / cytochrome c prime


Mass: 13407.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Plasmid: pet26b+ / 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-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 55.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2M Ammonium sulfate 0.1M 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 10, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→46.08 Å / Num. obs: 17754 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 12.7 / Num. measured all: 109533 / Scaling rejects: 105
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.736.50.8321100
9-46.084.60.031199.9

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLI

2yli


Resolution: 1.7→46.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.1113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 829 4.7 %RANDOM
Rwork0.2119 ---
obs0.214 16830 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.91 Å2 / Biso mean: 34.44 Å2 / Biso min: 21.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.7→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 59 108 1110
Biso mean--43.19 38.16 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021058
X-RAY DIFFRACTIONr_bond_other_d00.02965
X-RAY DIFFRACTIONr_angle_refined_deg2.3412.0571447
X-RAY DIFFRACTIONr_angle_other_deg3.68732226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16824.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39815158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.86155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211235
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02234
X-RAY DIFFRACTIONr_mcbond_it1.1461.966514
X-RAY DIFFRACTIONr_mcbond_other1.1461.957511
X-RAY DIFFRACTIONr_mcangle_it1.6582.928641
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 54 -
Rwork0.31 1205 -
all-1259 -
obs--99.68 %
Refinement TLS params.Method: refined / Origin x: 0.958 Å / Origin y: 41.645 Å / Origin z: 19.993 Å
111213212223313233
T0.1824 Å20.0237 Å2-0.0889 Å2-0.125 Å2-0.049 Å2--0.0645 Å2
L0.9116 °2-0.1106 °20.7251 °2-1.6524 °2-0.4502 °2--1.0289 °2
S-0.1297 Å °0.0872 Å °0.0394 Å °0.2086 Å °0.1371 Å °-0.2116 Å °-0.0861 Å °0.125 Å °-0.0074 Å °

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