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- PDB-6gbb: Copper nitrite reductase from Achromobacter cycloclastes: large c... -

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Basic information

Entry
Database: PDB / ID: 6gbb
TitleCopper nitrite reductase from Achromobacter cycloclastes: large cell polymorph dataset 1
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 / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 13, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)37,2334
Polymers37,0601
Non-polymers1733
Water2,126118
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)111,69912
Polymers111,1793
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 area13340 Å2
ΔGint-94 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.747, 97.747, 97.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 37059.809 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: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
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: 1.48→29.47 Å / Num. obs: 51981 / % possible obs: 100 % / Redundancy: 358 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.9946 / R split: 0.0743 / Net I/σ(I): 1.57
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 137 % / Mean I/σ(I) obs: 0.12 / Num. unique obs: 2561 / CC1/2: 0.487 / R split: 0.811 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6K

5i6k


Resolution: 1.48→29.47 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.08
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 2551 4.9 %RANDOM
Rwork0.2045 ---
obs0.2056 49430 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.14 Å2 / Biso mean: 23.28 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.48→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 5 118 2662
Biso mean--27.17 29.37 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192611
X-RAY DIFFRACTIONr_bond_other_d00.022325
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9413566
X-RAY DIFFRACTIONr_angle_other_deg3.81435385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3255332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54324.348115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8115380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5241510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212957
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02521
X-RAY DIFFRACTIONr_mcbond_it1.3182.2231331
X-RAY DIFFRACTIONr_mcbond_other1.312.221330
X-RAY DIFFRACTIONr_mcangle_it2.0683.3281662
LS refinement shellResolution: 1.48→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 180 -
Rwork0.426 3638 -
all-3818 -
obs--100 %

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