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- PDB-6qpt: Crystal structure of nitrite bound synthetic core domain of nitri... -

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Basic information

Entry
Database: PDB / ID: 6qpt
TitleCrystal structure of nitrite bound synthetic core domain of nitrite reductase from Ralstonia pickettii (residues 1-331)
ComponentsCopper-containing nitrite reductase
KeywordsMETAL BINDING PROTEIN / synthetic core domain / nitrite reductase / inter-copper electron transfer
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Nitrite reductase, copper-type / Cytochrome c / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin ...: / Nitrite reductase, copper-type / Cytochrome c / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAntonyuk, S.V. / Hedison, T.M. / Eady, R.R. / Hasnain, S.S. / Scrutton, N.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N019380/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis.
Authors: Hedison, T.M. / Shenoy, R.T. / Iorgu, A.I. / Heyes, D.J. / Fisher, K. / Wright, G.S.A. / Hay, S. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. / Scrutton, N.S.
History
DepositionFeb 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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_asym_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_asym_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_asym_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
D: Copper-containing nitrite reductase
E: Copper-containing nitrite reductase
F: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,00324
Polymers213,6686
Non-polymers1,33518
Water33,3101849
1
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,50212
Polymers106,8343
Non-polymers6689
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-73 kcal/mol
Surface area30530 Å2
MethodPISA
2
D: Copper-containing nitrite reductase
E: Copper-containing nitrite reductase
F: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,50212
Polymers106,8343
Non-polymers6689
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-77 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.910, 167.553, 143.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

21A-916-

HOH

31B-829-

HOH

41C-766-

HOH

51E-862-

HOH

61F-854-

HOH

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Components

#1: Protein
Copper-containing nitrite reductase


Mass: 35611.352 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Ralstonia pickettii (bacteria) / Strain: NCIMB 13142
References: UniProt: U3G913, UniProt: I6NAW4*PLUS, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-NO2 / NITRITE ION


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


Mass: 18.015 Da / Num. of mol.: 1849 / 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: 2.35 Å3/Da / Density % sol: 47.64 % / Description: fish skeleton
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 MgCl2, 20% P6000 in MES buffer pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2018 / Details: Mirrors
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.89→83 Å / Num. obs: 159198 / % possible obs: 99.9 % / Redundancy: 6.75 % / Biso Wilson estimate: 34.11 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.09 / Net I/σ(I): 5.3
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 6.57 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7889 / CC1/2: 0.485 / Rpim(I) all: 0.52 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.424 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22377 7566 4.8 %RANDOM
Rwork0.17834 ---
obs0.18048 149138 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14602 0 43 1849 16494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01315116
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713855
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.64620549
X-RAY DIFFRACTIONr_angle_other_deg1.2591.56932225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.68951935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11622.712708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.391152309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8891563
X-RAY DIFFRACTIONr_chiral_restr0.0560.21898
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023124
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_it0.6161.6987688
X-RAY DIFFRACTIONr_mcbond_other0.6151.6987686
X-RAY DIFFRACTIONr_mcangle_it1.0422.5399604
X-RAY DIFFRACTIONr_mcangle_other1.0412.5399604
X-RAY DIFFRACTIONr_scbond_it0.7321.8037427
X-RAY DIFFRACTIONr_scbond_other0.7321.8037428
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2172.6610933
X-RAY DIFFRACTIONr_long_range_B_refined4.5321.48116762
X-RAY DIFFRACTIONr_long_range_B_other4.5321.48316763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 569 -
Rwork0.286 10846 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6615-0.21860.36760.510.0611.27880.07690.0683-0.0845-0.0329-0.01430.05580.00380.0137-0.06250.02320.0046-0.0030.0093-0.00950.01641.68248.431-0.616
20.590.3447-0.18180.96050.03880.8308-0.05950.0472-0.0334-0.1220.04650.04350.028-0.01150.0130.0341-0.0181-0.00990.01350.0050.01234.4672.036-37.116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION1B1 - 601
3X-RAY DIFFRACTION1C1 - 601
4X-RAY DIFFRACTION2D1 - 601
5X-RAY DIFFRACTION2E1 - 601
6X-RAY DIFFRACTION2F1 - 601

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