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- PDB-9fom: CRYSTAL STRUCTURE OF AS-ISOLATED F295L MUTANT OF THREE-DOMAIN HEM... -

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Basic information

Entry
Database: PDB / ID: 9fom
TitleCRYSTAL STRUCTURE OF AS-ISOLATED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / HAEM AND CU CONTAINING NITRITE REDUCTASE / ELECTRON TRANSFER / REDOX REACTIONS / METAL BINDING PROTEIN
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Nitrite reductase, copper-type / Cytochrome c / Multicopper oxidase, N-terminal / Multicopper oxidase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.16 Å
AuthorsPetchyam, N. / Antonyuk, S.V. / Hasnain, S.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/N013972/1 United Kingdom
UK Research and Innovation (UKRI)BB/L006960/1 United Kingdom
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF AS-ISOLATED F295LMUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
Authors: Petchyam, N. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6604
Polymers49,9151
Non-polymers7463
Water13,745763
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,98012
Polymers149,7443
Non-polymers2,2379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17950 Å2
ΔGint-212 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.257, 128.257, 86.194
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1138-

HOH

21A-1241-

HOH

31A-1289-

HOH

41A-1319-

HOH

51A-1320-

HOH

61A-1335-

HOH

71A-1352-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49914.500 Da / Num. of mol.: 1 / Mutation: F295L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: nirK, D7S62_04310 / Plasmid: PET-26B F295L RpNiR / Details (production host): PET-26B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6NAW4, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.16→32.085 Å / Num. obs: 182213 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.052 / Rrim(I) all: 0.103 / Χ2: 0.84 / Net I/σ(I): 5.8
Reflection shellResolution: 1.16→1.18 Å / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.993 / Num. measured all: 31873 / Num. unique obs: 9100 / CC1/2: 0.433 / Rpim(I) all: 0.619 / Rrim(I) all: 1.176 / Χ2: 0.71 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.16→32.085 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.381 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.139 9199 5.05 %RANDOM
Rwork0.1143 172948 --
all0.116 ---
obs-182147 99.478 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.687 Å20.344 Å2-0 Å2
2--0.687 Å2-0 Å2
3----2.229 Å2
Refinement stepCycle: LAST / Resolution: 1.16→32.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 45 763 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163819
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.8515530
X-RAY DIFFRACTIONr_angle_other_deg0.7031.7628896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.756519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19810673
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.26410175
X-RAY DIFFRACTIONr_chiral_restr0.1090.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024852
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02908
X-RAY DIFFRACTIONr_nbd_refined0.2290.2735
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23395
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2580
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.231
X-RAY DIFFRACTIONr_nbd_other0.2060.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.278
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_mcbond_it4.3061.4171966
X-RAY DIFFRACTIONr_mcbond_other4.2441.4151965
X-RAY DIFFRACTIONr_mcangle_it5.692.5612488
X-RAY DIFFRACTIONr_mcangle_other5.6912.5622489
X-RAY DIFFRACTIONr_scbond_it6.6111.6382036
X-RAY DIFFRACTIONr_scbond_other6.6131.6392034
X-RAY DIFFRACTIONr_scangle_it8.9452.9122985
X-RAY DIFFRACTIONr_scangle_other8.9452.9122985
X-RAY DIFFRACTIONr_lrange_it20.6924.4264850
X-RAY DIFFRACTIONr_lrange_other16.08518.2674502
X-RAY DIFFRACTIONr_rigid_bond_restr4.53337821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.16-1.190.2717110.265128120.265135460.9520.95899.83020.266
1.19-1.2230.277400.247124380.248132050.9490.96599.79550.247
1.223-1.2580.2355790.232122310.232128330.9640.9799.82080.23
1.258-1.2970.2256430.214117680.214124330.9690.97599.82310.208
1.297-1.3390.2045770.191114720.192120800.9760.9899.74340.182
1.339-1.3860.2056050.164110410.166116690.9760.98699.80290.153
1.386-1.4380.1665590.147106960.148112730.9820.98899.84030.134
1.438-1.4970.1545140.127102740.129108290.9850.99199.62140.115
1.497-1.5630.1465360.10998570.111104110.9870.99499.82710.098
1.563-1.640.1385030.09794190.199350.990.99599.86910.087
1.64-1.7280.1194520.08589430.08694310.9920.99699.61830.076
1.728-1.8330.1194350.08184710.08389450.9910.99799.5640.075
1.833-1.9590.1144060.08179670.08384260.9930.99799.3710.078
1.959-2.1150.1123660.08873720.08977970.9930.99799.24330.087
2.115-2.3160.1083640.0868070.08172260.9940.99799.23890.081
2.316-2.5870.0953400.07461070.07564980.9940.99799.21510.078
2.587-2.9840.1142540.08554260.08757500.9920.99698.78260.093
2.984-3.6470.1132820.09444750.09548610.9920.99597.86050.107
3.647-5.1250.1312350.10934100.1137700.9930.99496.68430.129
5.125-32.0850.202980.17719620.17821240.9830.98696.98680.205

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