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- PDB-5og4: Cu nitrite reductase serial data at varying temperatures RT 0.18MGy -

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Basic information

Entry
Database: PDB / ID: 5og4
TitleCu nitrite reductase serial data at varying temperatures RT 0.18MGy
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Electron transfer / 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 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / 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 / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHorrell, S. / Kekilli, D. / Strange, R.W. / Hough, M.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022714/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M020924/1 United Kingdom
Leverhulme TrustRPG-2014-355 United Kingdom
CitationJournal: IUCrJ / Year: 2018
Title: Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.
Authors: Horrell, S. / Kekilli, D. / Sen, K. / Owen, R.L. / Dworkowski, F.S.N. / Antonyuk, S.V. / Keal, T.W. / Yong, C.W. / Eady, R.R. / Hasnain, S.S. / Strange, R.W. / Hough, M.A.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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)37,06710
Polymers36,6211
Non-polymers4469
Water2,702150
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)111,20230
Polymers109,8643
Non-polymers1,33927
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15510 Å2
ΔGint-84 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.255, 96.255, 96.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

21A-750-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36621.332 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 (E. coli) / References: UniProt: P25006, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.76→55.58 Å / Num. obs: 29589 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rpim(I) all: 0.089 / Net I/σ(I): 5
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.52 / Rpim(I) all: 0.513 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata collection
XDSVERSION Oct 15, 2015data reduction
Aimless0.5.17data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6K

5i6k


Resolution: 1.76→55.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.691 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.20258 1525 5.2 %RANDOM
Rwork0.17151 ---
obs0.17317 27974 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.056 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.76→55.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 23 150 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192702
X-RAY DIFFRACTIONr_bond_other_d0.0070.022448
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9473669
X-RAY DIFFRACTIONr_angle_other_deg1.02335682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56524.132121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56815414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213040
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02545
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5472.0091351
X-RAY DIFFRACTIONr_mcbond_other1.5472.0061348
X-RAY DIFFRACTIONr_mcangle_it2.36931692
X-RAY DIFFRACTIONr_mcangle_other2.3693.0011693
X-RAY DIFFRACTIONr_scbond_it2.2772.3371350
X-RAY DIFFRACTIONr_scbond_other2.2242.3171341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6553.3551972
X-RAY DIFFRACTIONr_long_range_B_refined5.58323.9322798
X-RAY DIFFRACTIONr_long_range_B_other5.5823.9142797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 113 -
Rwork0.335 2038 -
obs--99.22 %

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