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- PDB-4d4n: Nitrosyl complex of the D121A variant of cytochrome c prime from ... -

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Basic information

Entry
Database: PDB / ID: 4d4n
TitleNitrosyl complex of the D121A variant of cytochrome c prime from Alcaligenes xylosoxidans
ComponentsCYTOCHROME C'
KeywordsOXIDOREDUCTASE / PROXIMAL NO / GAS SENSING
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 / NITRIC OXIDE / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.45 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
DepositionOct 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
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

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Assembly

Deposited unit
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2363
Polymers13,5871
Non-polymers6492
Water2,648147
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4726
Polymers27,1752
Non-polymers1,2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1450 Å2
ΔGint-18.9 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.756, 53.756, 180.023
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-2027-

HOH

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Components

#1: Protein CYTOCHROME C' / CYTOCHROME C PRIME


Mass: 13587.433 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


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


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


Mass: 18.015 Da / Num. of mol.: 147 / 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 % / 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: 1.45→9.3 Å / Num. obs: 27816 / % possible obs: 97.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.45→46.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.872 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20074 1399 5 %RANDOM
Rwork0.15919 ---
obs0.1613 26396 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.31 Å20 Å2
2---0.61 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 45 147 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021030
X-RAY DIFFRACTIONr_bond_other_d0.0010.02959
X-RAY DIFFRACTIONr_angle_refined_deg2.2592.0461411
X-RAY DIFFRACTIONr_angle_other_deg1.84432207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9625132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43524.65143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20915156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.37155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211255
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02230
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_it3.4452.295508
X-RAY DIFFRACTIONr_mcbond_other3.4112.29506
X-RAY DIFFRACTIONr_mcangle_it3.8553.455634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0552.532522
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_restr5.51531988
X-RAY DIFFRACTIONr_sphericity_free32.747528
X-RAY DIFFRACTIONr_sphericity_bonded16.34252077
LS refinement shellResolution: 1.449→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 94 -
Rwork0.209 1871 -
obs--96.7 %

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