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- PDB-5nc0: The 0.91 A resolution structure of the L16G mutant of cytochrome ... -

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Basic information

Entry
Database: PDB / ID: 5nc0
TitleThe 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide
ComponentsCytochrome c'
KeywordsOXIDOREDUCTASE / nitric oxide / cytochrome / homodimer
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 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
HEME C / NITRIC OXIDE / NITRITE ION / NITRATE ION / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å
AuthorsStrange, R. / Hough, M. / Antonyuk, S. / Rustage, N.
CitationJournal: Inorg Chem / Year: 2017
Title: Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory.
Authors: Nilsson, Z.N. / Mandella, B.L. / Sen, K. / Kekilli, D. / Hough, M.A. / Moenne-Loccoz, P. / Strange, R.W. / Andrew, C.R.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 3.0Aug 26, 2026Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)14,95013
Polymers13,5751
Non-polymers1,37512
Water4,143230
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,90126
Polymers27,1512
Non-polymers2,75024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area7270 Å2
ΔGint-141 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.430, 52.430, 183.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c'


Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: L16G
Source method: isolated from a genetically manipulated source
Details: residue PCA is pyroglutamic acid - 2-pyrrolidone-5-carboxylic acid
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00138

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Non-polymers , 7 types, 242 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: AMMONIUM SULPHATE, TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.7872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7872 Å / Relative weight: 1
ReflectionResolution: 0.91→44.07 Å / Num. obs: 106845 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1
Reflection shellResolution: 0.91→0.93 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4889 / CC1/2: 0.547 / Rpim(I) all: 0.564 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS20161101data reduction
Aimless0.5.27data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YL7

2yl7


Resolution: 0.91→44.07 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.378 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13177 5378 5 %RANDOM
Rwork0.12453 ---
obs0.1249 101466 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 0.91→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 87 230 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021091
X-RAY DIFFRACTIONr_bond_other_d0.0030.02991
X-RAY DIFFRACTIONr_angle_refined_deg2.4712.0771484
X-RAY DIFFRACTIONr_angle_other_deg1.07532306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77424.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01715170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.307155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
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_it0.7160.598521
X-RAY DIFFRACTIONr_mcbond_other0.6230.593518
X-RAY DIFFRACTIONr_mcangle_it0.9760.9653
X-RAY DIFFRACTIONr_mcangle_other0.9840.904654
X-RAY DIFFRACTIONr_scbond_it1.530.839570
X-RAY DIFFRACTIONr_scbond_other1.530.839570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8161.169827
X-RAY DIFFRACTIONr_long_range_B_refined2.5789.4241366
X-RAY DIFFRACTIONr_long_range_B_other2.5779.431367
X-RAY DIFFRACTIONr_rigid_bond_restr5.07532081
X-RAY DIFFRACTIONr_sphericity_free19.6535156
X-RAY DIFFRACTIONr_sphericity_bonded6.35452149
LS refinement shellResolution: 0.91→0.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 359 -
Rwork0.273 7086 -
obs--95.31 %

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