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- PDB-9fuj: CRYSTAL STRUCTURE OF REDUCED F295L MUTANT OF THREE-DOMAIN HEME-CU... -

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Basic information

Entry
Database: PDB / ID: 9fuj
TitleCRYSTAL STRUCTURE OF REDUCED 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: 1.331 Å
AuthorsPetchyam, N. / Antonyuk, S. / 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 REDUCED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 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
Water12,448691
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 area17900 Å2
ΔGint-211 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.961, 127.961, 86.602
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1071-

HOH

21A-1136-

HOH

31A-1216-

HOH

41A-1263-

HOH

51A-1273-

HOH

61A-1285-

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 / 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.: 691 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
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% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.80001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.80001 Å / Relative weight: 1
ReflectionResolution: 1.33→37.74 Å / Num. obs: 116526 / % possible obs: 96.1 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.096 / Χ2: 0.94 / Net I/σ(I): 8
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4314 / CC1/2: 0.363 / Rpim(I) all: 0.754 / Rrim(I) all: 1.319 / Χ2: 0.92 / % possible all: 71.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.331→37.735 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / WRfactor Rfree: 0.132 / WRfactor Rwork: 0.104 / SU B: 1.845 / SU ML: 0.031 / Average fsc free: 0.9792 / Average fsc work: 0.9849 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 5922 5.085 %RANDOM
Rwork0.1118 110529 --
all0.113 ---
obs-116451 96.07 %-
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: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.182 Å20.091 Å2-0 Å2
2--0.182 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.331→37.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 45 691 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124039
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163818
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.855575
X-RAY DIFFRACTIONr_angle_other_deg0.6571.7598887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1265568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.977519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94710671
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.57710178
X-RAY DIFFRACTIONr_chiral_restr0.0990.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024889
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02915
X-RAY DIFFRACTIONr_nbd_refined0.2610.2762
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23332
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21839
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2506
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.229
X-RAY DIFFRACTIONr_nbd_other0.2030.2135
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.268
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_mcbond_it4.6361.4851987
X-RAY DIFFRACTIONr_mcbond_other4.4151.4841987
X-RAY DIFFRACTIONr_mcangle_it6.2432.682514
X-RAY DIFFRACTIONr_mcangle_other6.312.6832515
X-RAY DIFFRACTIONr_scbond_it5.9131.6822052
X-RAY DIFFRACTIONr_scbond_other5.9141.6832050
X-RAY DIFFRACTIONr_scangle_it8.3993.0083010
X-RAY DIFFRACTIONr_scangle_other8.3993.0073010
X-RAY DIFFRACTIONr_lrange_it18.03322.0784794
X-RAY DIFFRACTIONr_lrange_other13.79217.5774508
X-RAY DIFFRACTIONr_rigid_bond_restr4.00737857
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
1.331-1.3660.3123370.30561970.30689620.940.93972.90780.308
1.366-1.4030.3073900.27867010.2887280.9430.95381.24430.279
1.403-1.4440.2673740.2575010.2585450.9560.96392.15920.247
1.444-1.4880.2443950.2178350.21282480.9680.97699.78180.202
1.488-1.5370.2034490.16274980.16479480.9750.98599.98740.151
1.537-1.590.1683540.13274150.13377710.9840.9999.97430.12
1.59-1.650.1583650.11570590.11774250.9850.99299.98650.104
1.65-1.7180.1443680.10268030.10471720.9880.99499.98610.091
1.718-1.7940.1453250.09365500.09568770.9870.99599.97090.083
1.794-1.8810.1263360.08162970.08366330.9910.9961000.074
1.881-1.9830.1173170.08259130.08462300.9920.9971000.077
1.983-2.1030.1253200.08755910.08959110.9910.9971000.083
2.103-2.2470.0992840.0853060.08155900.9940.9971000.077
2.247-2.4270.1132410.07649140.07851550.9920.9971000.073
2.427-2.6570.0982850.07544940.07647790.9940.9971000.073
2.657-2.9690.1152250.08340920.08543170.9910.9961000.082
2.969-3.4250.1131760.09236310.09338070.9920.9951000.093
3.425-4.1860.1171860.09430420.09532280.9920.9951000.099
4.186-5.8830.141140.13123630.13224770.9930.9941000.137
5.883-37.7350.219810.20213270.20314080.980.9831000.225

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