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- PDB-6qwg: Serial Femtosecond Crystallography Structure of Cu Nitrite Reduct... -

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Basic information

Entry
Database: PDB / ID: 6qwg
TitleSerial Femtosecond Crystallography Structure of Cu Nitrite Reductase from Achromobacter cycloclastes: Nitrite complex at Room Temperature
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper nitrite reductase / serial femtosecond crystallography / ligand binding / damage free structure
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEbrahim, A.E. / Moreno-Chicano, T. / Appleby, M.V. / Worrall, J.W. / Duyvesteyn, H.M.E. / Strange, R.W. / Beale, J. / Axford, D. / Sherrell, D.A. / Sugimoto, H. ...Ebrahim, A.E. / Moreno-Chicano, T. / Appleby, M.V. / Worrall, J.W. / Duyvesteyn, H.M.E. / Strange, R.W. / Beale, J. / Axford, D. / Sherrell, D.A. / Sugimoto, H. / Owada, S. / Tono, K. / Owen, R.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022714/1 United Kingdom
Leverhulme TrustRPG-2014-0355 United Kingdom
CitationJournal: Iucrj / Year: 2019
Title: High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.
Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / ...Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / Tono, K. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,6954
Polymers36,5221
Non-polymers1733
Water2,162120
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)110,08612
Polymers109,5673
Non-polymers5199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area13440 Å2
ΔGint-93 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.600, 97.600, 97.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-620-

HOH

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Components

#1: Protein Copper-containing nitrite reductase / Cu-NIR


Mass: 36522.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)
#2: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.12 Å3/Da / Density % sol: 42.02 % / Description: Microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5
Details: 20 mg per ml AcNiR in 20 mM Tris HCl pH 7.5 mixed with 2.5 M ammonium sulfate, 0.1 M sodium citrate pH 4.5 in a ratio of 1 to 3 and mixed by vortexing for 60sec

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Data collection

DiffractionMean temperature: 301 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.23 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 1.9→43.65 Å / Num. obs: 24729 / % possible obs: 99.9 % / Redundancy: 3281 % / CC1/2: 0.99 / R split: 0.0973 / Net I/σ(I): 0
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 2438 / CC1/2: 0.63 / R split: 0.586 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GB8

6gb8


Resolution: 1.9→43.648 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.4
RfactorNum. reflection% reflection
Rfree0.1723 1001 4.05 %
Rwork0.1368 --
obs0.1382 24698 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.82 Å2 / Biso mean: 37.1104 Å2 / Biso min: 24.35 Å2
Refinement stepCycle: final / Resolution: 1.9→43.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 5 120 2699
Biso mean--39.27 43.52 -
Num. residues----333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9003-2.00040.31851420.239833563498
2.0004-2.12580.20571390.151133433482
2.1258-2.28990.18621420.143533523494
2.2899-2.52030.2321430.149733523495
2.5203-2.8850.20131410.152533923533
2.885-3.63450.16671440.135634013545
3.6345-43.65950.13761500.118435013651

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