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- PDB-7r2u: CRYSTAL STRUCTURE OF AS-ISOLATED Q262N MUTANT OF THREE-DOMAIN HEM... -

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Basic information

Entry
Database: PDB / ID: 7r2u
TitleCRYSTAL STRUCTURE OF AS-ISOLATED Q262N 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: 1.5 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: Structural and biochemical studies of three-domain haem CuNiR from Ralstonia pickettii mutants
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.
History
DepositionFeb 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6804
Polymers49,9341
Non-polymers7463
Water11,043613
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)152,04012
Polymers149,8033
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 area18100 Å2
ΔGint-211 kcal/mol
Surface area44520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.650, 127.650, 86.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1142-

HOH

21A-1208-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49934.488 Da / Num. of mol.: 1 / Mutation: Q262N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: RP6297_03937 / 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
#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.: 613 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
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: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2021 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.5→37.63 Å / Num. obs: 83956 / % possible obs: 100 % / Redundancy: 5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.054 / Rrim(I) all: 0.121 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 5 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.531.3241.241610.4310.6591.481100
8.22-37.610.06723.75140.9930.0330.07599.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
AutoProcessphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZIY

3ziy


Resolution: 1.5→37.63 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.976 / SU B: 3.455 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 4134 4.9 %RANDOM
Rwork0.1054 ---
obs0.1076 79820 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.43 Å2 / Biso mean: 24.346 Å2 / Biso min: 10.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å2-0 Å2
2--1.41 Å2-0 Å2
3----4.58 Å2
Refinement stepCycle: final / Resolution: 1.5→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 77 639 4155
Biso mean--17.92 42.24 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0124109
X-RAY DIFFRACTIONr_bond_other_d0.0050.0163912
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.6625693
X-RAY DIFFRACTIONr_angle_other_deg0.6911.5749126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1423.4200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40315692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3591519
X-RAY DIFFRACTIONr_chiral_restr0.1310.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024909
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02934
X-RAY DIFFRACTIONr_rigid_bond_restr4.52338020
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 335 -
Rwork0.267 5901 -
all-6236 -
obs--99.94 %

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