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- PDB-5i6m: Crystal Structure of Copper Nitrite Reductase at 100K after 7.59 MGy -

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Basic information

Entry
Database: PDB / ID: 5i6m
TitleCrystal Structure of Copper Nitrite Reductase at 100K after 7.59 MGy
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Copper Nitrite Reductase / Reaction Mechanism / Serial Crystallography
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
ACETATE ION / COPPER (II) ION / MALONATE ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsHorrell, S. / Hough, M.A. / Strange, R.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M020924/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M022714/1 United Kingdom
CitationJournal: Iucrj / Year: 2016
Title: Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.
Authors: Horrell, S. / Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S. / Hough, M.A. / Strange, R.W.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 10, 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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)37,03113
Polymers36,3911
Non-polymers64012
Water5,873326
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)111,09439
Polymers109,1733
Non-polymers1,92136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15910 Å2
ΔGint-78 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.155, 95.155, 95.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36391.008 Da / Num. of mol.: 1 / Fragment: Copper Nitrite Reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)

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Non-polymers , 6 types, 338 molecules

#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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO2
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.02 Å3/Da / Density % sol: 38.98 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.5
Details: 1.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.09→42.6 Å / Num. obs: 115628 / % possible obs: 97.5 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.022 / Rrim(I) all: 0.048 / Net I/σ(I): 15.9 / Num. measured all: 465148
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.09-1.113.30.9251845356500.5590.5781.0971.296.8
5.97-42.554.70.02332506910.9980.0110.02666.588.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWI

2bwi


Resolution: 1.09→42.6 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.863 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1463 5751 5 %RANDOM
Rwork0.1267 ---
obs0.1276 109866 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.51 Å2 / Biso mean: 14.488 Å2 / Biso min: 6.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.09→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 36 330 2932
Biso mean--29.18 26.49 -
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192894
X-RAY DIFFRACTIONr_bond_other_d0.0020.022678
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9543929
X-RAY DIFFRACTIONr_angle_other_deg1.04936188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0625367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5924.586133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4315453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1811512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213311
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02647
X-RAY DIFFRACTIONr_mcbond_it1.2511.1961431
X-RAY DIFFRACTIONr_mcbond_other1.2381.1921428
X-RAY DIFFRACTIONr_mcangle_it1.5521.7991794
X-RAY DIFFRACTIONr_rigid_bond_restr2.10335569
X-RAY DIFFRACTIONr_sphericity_free32.364560
X-RAY DIFFRACTIONr_sphericity_bonded7.83555762
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 397 -
Rwork0.274 8099 -
all-8496 -
obs--97.04 %

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