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- PDB-6qpx: Crystal structure of nitrite bound Y323A mutant of haem-Cu contai... -

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Basic information

Entry
Database: PDB / ID: 6qpx
TitleCrystal structure of nitrite bound Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
ComponentsCopper-containing nitrite reductase
KeywordsMETAL BINDING PROTEIN / haem and Cu containing 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
: / Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. ...: / Cytochrome C oxidase, cbb3-type, subunit III / Nitrite reductase, copper-type / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / NITRITE ION / Copper-containing nitrite reductase / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsAntonyuk, S.V. / Shenoy, R.T. / 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 1.2Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.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
I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,29610
Polymers99,7132
Non-polymers1,5838
Water21,1501174
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)151,94415
Polymers149,5693
Non-polymers2,37512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18440 Å2
ΔGint-205 kcal/mol
Surface area44590 Å2
MethodPISA
2
I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules

I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,94415
Polymers149,5693
Non-polymers2,37512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18440 Å2
ΔGint-206 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.500, 128.500, 172.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1159-

HOH

21A-1161-

HOH

31A-1166-

HOH

41A-1167-

HOH

51A-1173-

HOH

61A-1176-

HOH

71I-1045-

HOH

81I-1089-

HOH

91I-1140-

HOH

101I-1182-

HOH

111I-1185-

HOH

121I-1189-

HOH

131I-1196-

HOH

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 49856.422 Da / Num. of mol.: 2 / Mutation: Y323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: NCIMB 13142 / Gene: HMPREF0989_00586 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: U3G913, UniProt: I6NAW4*PLUS, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2018
RadiationMonochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.61→30.1 Å / Num. obs: 137234 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 14.878 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.071 / Net I/av σ(I): 7.6 / Net I/σ(I): 0.997
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 5 % / Rmerge(I) obs: 1.8 / Num. unique obs: 6817 / CC1/2: 0.448 / Rpim(I) all: 0.89 / Χ2: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.7→29.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.972 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20303 5447 4.7 %RANDOM
Rwork0.1738 ---
obs0.17518 111132 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.7→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 96 1174 8109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176673
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6669971
X-RAY DIFFRACTIONr_angle_other_deg1.3631.58315561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2665960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05723.255341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.037151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5661532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028365
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021471
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_it0.741.4043694
X-RAY DIFFRACTIONr_mcbond_other0.7371.4023693
X-RAY DIFFRACTIONr_mcangle_it1.2282.0994630
X-RAY DIFFRACTIONr_mcangle_other1.2282.14631
X-RAY DIFFRACTIONr_scbond_it1.131.5323593
X-RAY DIFFRACTIONr_scbond_other1.1291.5313589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8382.2355315
X-RAY DIFFRACTIONr_long_range_B_refined5.9819.2638395
X-RAY DIFFRACTIONr_long_range_B_other5.46117.4548003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 418 -
Rwork0.373 8260 -
obs--99.98 %
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)
10.7083-0.38350.2780.6671-0.2820.47640.001-0.0146-0.0947-0.0168-0.02040.0380.0633-0.04910.01940.0188-0.01620.01370.0185-0.00960.0235-10.782-16.063-0.595
20.97380.2139-0.38710.3392-0.0980.39120.01330.02010.08690.0093-0.01510.0638-0.0477-0.02730.00170.02420.0058-0.00820.0038-0.0050.0216-8.588-56.819-27.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 701
2X-RAY DIFFRACTION2I5 - 701

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