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- PDB-5ngx: The 1.06 A resolution structure of the L16G mutant of ferric cyto... -

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Basic information

Entry
Database: PDB / ID: 5ngx
TitleThe 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite
ComponentsCytochrome c'
KeywordsOXIDOREDUCTASE / nitrite / cytochrome / homodimer / ferric / heme
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / 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
HEME C / NITRITE ION / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsStrange, R. / Hough, M. / Kekelli, D. / Horrell, S. / Moreno Chicano, T.
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 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2019Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Polymer sequence
Category: atom_site / citation ...atom_site / citation / citation_author / entity_poly / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year / _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 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,2034
Polymers13,4461
Non-polymers7573
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-17 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 53.910, 183.210
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-465-

HOH

21A-506-

HOH

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Components

#1: Protein Cytochrome c'


Mass: 13446.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM sodium nitrite, 2.2 M ammonium sulphate and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.06→45.24 Å / Num. obs: 70168 / % possible obs: 96.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 8.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.023 / Net I/σ(I): 13.1
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 5.1 % / Num. unique obs: 3511 / CC1/2: 0.587 / Rpim(I) all: 0.493 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.5.179-gfd2bada8-dials-1.4data reduction
Aimless0.5.31data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yl7

2yl7


Resolution: 1.06→45.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.121 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20005 3506 5 %RANDOM
Rwork0.17758 ---
obs0.1787 66609 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----2.08 Å2
Refinement stepCycle: 1 / Resolution: 1.06→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 52 214 1211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191127
X-RAY DIFFRACTIONr_bond_other_d0.0010.021005
X-RAY DIFFRACTIONr_angle_refined_deg2.1792.0011549
X-RAY DIFFRACTIONr_angle_other_deg1.45732342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5772548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83815170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.306155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211326
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02235
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_it1.051.211556
X-RAY DIFFRACTIONr_mcbond_other1.0441.206555
X-RAY DIFFRACTIONr_mcangle_it1.3841.826703
X-RAY DIFFRACTIONr_mcangle_other1.3841.83704
X-RAY DIFFRACTIONr_scbond_it1.491.356571
X-RAY DIFFRACTIONr_scbond_other1.4851.355571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7331.955843
X-RAY DIFFRACTIONr_long_range_B_refined3.65316.0451398
X-RAY DIFFRACTIONr_long_range_B_other3.65116.0331398
X-RAY DIFFRACTIONr_rigid_bond_restr5.73632131
X-RAY DIFFRACTIONr_sphericity_free24.6085155
X-RAY DIFFRACTIONr_sphericity_bonded8.70552166
LS refinement shellResolution: 1.06→1.088 Å
RfactorNum. reflection% reflection
Rfree0.348 271 -
Rwork0.352 4919 -
obs--99.05 %

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