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- PDB-5agf: Nitrosyl complex of the D121Q variant of cytochrome c prime from ... -

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Basic information

Entry
Database: PDB / ID: 5agf
TitleNitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans
ComponentsCYTOCHROME C PRIME
KeywordsOXIDOREDUCTASE / PROXIMAL NO / CYTOCHROME / GAS SENSING / 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 class II profile. / Cytochrome C' / Cytochrome c, class II / Cytochrome c prime / 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 / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.09 Å
AuthorsGahfoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Hough, M.A. / Strange, R.W.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Hydrogen Bonding of the Dissociated Histidine Ligand is not Required for Formation of a Proximal No Adduct in Cytochrome C'.
Authors: Ghafoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Strange, R.W. / Hough, M.A.
History
DepositionJan 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Atomic model / Other
Revision 1.2Dec 7, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 2.0Mar 11, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3894
Polymers13,6441
Non-polymers7453
Water3,495194
1
A: CYTOCHROME C PRIME
hetero molecules

A: CYTOCHROME C PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7788
Polymers27,2892
Non-polymers1,4896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1460 Å2
ΔGint-28.6 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.239, 53.239, 180.539
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-2039-

HOH

21A-2057-

HOH

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Components

#1: Protein CYTOCHROME C PRIME


Mass: 13644.483 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#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.: 194 / 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: 2.64 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULFATE, HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013 / Details: MIRRORS
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→15.5 Å / Num. obs: 62452 / % possible obs: 97 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 1.09→1.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.09→46.11 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.351 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18521 3155 5.1 %RANDOM
Rwork0.1695 ---
obs0.17029 59145 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å20 Å2
2---0.39 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.09→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 50 194 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021156
X-RAY DIFFRACTIONr_bond_other_d0.0030.021062
X-RAY DIFFRACTIONr_angle_refined_deg2.272.041594
X-RAY DIFFRACTIONr_angle_other_deg1.80132463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03825.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.558154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211429
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02257
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_it3.6261.515571
X-RAY DIFFRACTIONr_mcbond_other3.6261.513569
X-RAY DIFFRACTIONr_mcangle_it4.8152.308722
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2591.606585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.28932218
X-RAY DIFFRACTIONr_sphericity_free70.497523
X-RAY DIFFRACTIONr_sphericity_bonded15.87452355
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 145 -
Rwork0.295 3163 -
obs--71.66 %

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