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- PDB-7qq2: CRYSTAL STRUCTURE OF AS-ISOLATED S321M MUTANT OF THREE-DOMAIN HEM... -

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Basic information

Entry
Database: PDB / ID: 7qq2
TitleCRYSTAL STRUCTURE OF AS-ISOLATED S321M 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPetchyam, N. / Antonyuk, S. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: To Be Published
Title: Structural studies of haem three-domain copper nitrite reductase mutants from Ralstonia pickettii
Authors: Petchyam, N. / Antonyuk, S. / Hasnain, S.S.
History
DepositionJan 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7384
Polymers49,9931
Non-polymers7463
Water7,728429
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)152,21512
Polymers149,9783
Non-polymers2,2379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18130 Å2
ΔGint-213 kcal/mol
Surface area44040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.140, 180.140, 180.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

21A-979-

HOH

31A-994-

HOH

41A-1013-

HOH

51A-1020-

HOH

61A-1021-

HOH

71A-1022-

HOH

81A-1025-

HOH

91A-1029-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49992.633 Da / Num. of mol.: 1 / Mutation: S321M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Gene: RP6297_03937 / Production host: Escherichia coli BL21 (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.: 429 / 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

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: I04-1 / Wavelength: 0.9126 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 2.1→73.65 Å / Num. obs: 56514 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.06 / Rrim(I) all: 0.129 / Net I/av σ(I): 8.1 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.164.71.0111.546410.5460.5221.141100
8.91-73.544.50.03524.48030.9980.0180.0499.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZIY

3ziy


Resolution: 2.1→73.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.997 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2974 5.3 %RANDOM
Rwork0.1534 ---
obs0.1551 53484 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.56 Å2 / Biso mean: 34.351 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→73.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 45 433 3915
Biso mean--40.82 42.9 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153400
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.6684982
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5897853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7555473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81123.023172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.841517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024241
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02814
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 211 -
Rwork0.255 3896 -
all-4107 -
obs--100 %

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