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- PDB-6gcg: Copper nitrite reductase from Achromobacter cycloclastes: large p... -

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Basic information

Entry
Database: PDB / ID: 6gcg
TitleCopper nitrite reductase from Achromobacter cycloclastes: large polymorph dataset 15
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper / denitrification / serial synchrotron crystallography / polymorphs / nitrite reductase
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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80015244154 Å
AuthorsEbrahim, A. / Appleby, M.V. / Axford, D. / Beale, J. / Moreno-Chicano, T. / Sherrell, D.A. / Strange, R.W. / Owen, R.L. / Hough, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022714/1 United Kingdom
Leverhulme TrustRPG-2014-355 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography.
Authors: Ebrahim, A. / Appleby, M.V. / Axford, D. / Beale, J. / Moreno-Chicano, T. / Sherrell, D.A. / Strange, R.W. / Hough, M.A. / Owen, R.L.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 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)40,9463
Polymers40,8191
Non-polymers1272
Water2,036113
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)122,8399
Polymers122,4583
Non-polymers3816
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 area12950 Å2
ΔGint-100 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.989, 97.989, 97.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

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


Mass: 40819.172 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-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.15 Å3/Da / Density % sol: 42.71 % / Description: Microcrystals
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.5
Details: Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5 M ammonium sulphate, 0.1 M sodium citrate pH 4.5 buffer, in a ratio of ...Details: Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5 M ammonium sulphate, 0.1 M sodium citrate pH 4.5 buffer, in a ratio of 1:3 and mixed by vortexing for 60 seconds. Microcrystals with a diameter of 5-15 microns grew at room temperature over a period of 4-6 days.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→29.55 Å / Num. obs: 29321 / % possible obs: 100 % / Redundancy: 978 % / Biso Wilson estimate: 15.5148580083 Å2 / CC1/2: 0.999 / R split: 0.0583 / Net I/σ(I): 0.72
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 799 % / Mean I/σ(I) obs: 0.06 / Num. unique obs: 1733 / CC1/2: 0.502 / R split: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALSdata reduction
REFMACrefinement
PHENIX1.12_2829refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i6k

5i6k


Resolution: 1.80015244154→29.5446443882 Å / SU ML: 0.229445962341 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2277153153
RfactorNum. reflection% reflectionSelection details
Rfree0.205036675018 1581 5.39203983493 %RANDOM
Rwork0.166235283904 ---
obs0.168374479402 29321 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.7443443621 Å2
Refinement stepCycle: LAST / Resolution: 1.80015244154→29.5446443882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 2 113 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006305266675722604
X-RAY DIFFRACTIONf_angle_d0.8848362022213562
X-RAY DIFFRACTIONf_chiral_restr0.0577525434176397
X-RAY DIFFRACTIONf_plane_restr0.00557028246372470
X-RAY DIFFRACTIONf_dihedral_angle_d12.39005972131512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.85820.3786296715741540.3522866451862497X-RAY DIFFRACTION100
1.8582-1.92470.4112648122061510.3283292959482494X-RAY DIFFRACTION100
1.9247-2.00170.3280525427051320.2537789334422480X-RAY DIFFRACTION100
2.0017-2.09280.2662145467081740.2189032064272475X-RAY DIFFRACTION100
2.0928-2.20310.2381196453511500.1870196539852477X-RAY DIFFRACTION100
2.2031-2.3410.2173714853371400.1752528618162515X-RAY DIFFRACTION100
2.341-2.52170.2319861117021120.1752870175872549X-RAY DIFFRACTION100
2.5217-2.77530.2074093429821310.1733248302882528X-RAY DIFFRACTION100
2.7753-3.17650.2110527719631380.1606854360122534X-RAY DIFFRACTION100
3.1765-4.00050.1544760944071530.1368154723572548X-RAY DIFFRACTION100
4.0005-29.54860.1587556087111460.1273150870532643X-RAY DIFFRACTION100

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