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- PDB-5of7: Cu nitrite reductase serial data at varying temperatures 190K 0.48MGy -

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Basic information

Entry
Database: PDB / ID: 5of7
TitleCu nitrite reductase serial data at varying temperatures 190K 0.48MGy
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 / MALONATE ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry / reflns
Item: _reflns.B_iso_Wilson_estimate / _reflns.pdbx_Rpim_I_all
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_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

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72318
Polymers36,6211
Non-polymers1,10217
Water5,945330
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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)113,16954
Polymers109,8643
Non-polymers3,30551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area20350 Å2
ΔGint-287 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.940, 94.940, 94.940
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-629-

HOH

21A-811-

HOH

31A-822-

HOH

41A-823-

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 , 7 types, 347 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
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: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.27→42.46 Å / Num. obs: 75137 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.033 / Net I/σ(I): 12.2
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.36 / Rpim(I) all: 0.697 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION Oct 15, 2015data reduction
Aimless0.5.18data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I6K

5i6k


Resolution: 1.27→42.46 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.977 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 3707 4.9 %RANDOM
Rwork0.12374 ---
obs0.1256 71387 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.707 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.27→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 60 330 2971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192785
X-RAY DIFFRACTIONr_bond_other_d00.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9633806
X-RAY DIFFRACTIONr_angle_other_deg3.91135859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5415359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30124.48125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213124
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02544
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_it1.7361.4521372
X-RAY DIFFRACTIONr_mcbond_other1.7011.4441366
X-RAY DIFFRACTIONr_mcangle_it2.1522.1841716
X-RAY DIFFRACTIONr_mcangle_other2.1512.1871717
X-RAY DIFFRACTIONr_scbond_it2.8031.7941413
X-RAY DIFFRACTIONr_scbond_other2.7821.7941409
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4522.5852078
X-RAY DIFFRACTIONr_long_range_B_refined4.21519.2863025
X-RAY DIFFRACTIONr_long_range_B_other3.79918.5472962
X-RAY DIFFRACTIONr_rigid_bond_restr6.75335299
X-RAY DIFFRACTIONr_sphericity_free24.0895215
X-RAY DIFFRACTIONr_sphericity_bonded8.9255361
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 270 -
Rwork0.281 5264 -
obs--100 %

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