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- PDB-6qpu: Crystal structure of as isolated synthetic core domain of nitrite... -

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Basic information

Entry
Database: PDB / ID: 6qpu
TitleCrystal structure of as isolated 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 / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia sp. 5_2_56FAA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2Jan 24, 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_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)215,22627
Polymers213,6686
Non-polymers1,55821
Water19,1321062
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)107,71014
Polymers106,8343
Non-polymers87611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-106 kcal/mol
Surface area30620 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)107,51613
Polymers106,8343
Non-polymers68210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-119 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.884, 167.520, 143.982
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-745-

HOH

21D-723-

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 genetically manipulated source
Source: (gene. exp.) Ralstonia sp. 5_2_56FAA (bacteria) / Gene: HMPREF0989_00586 / Cell line (production host): BL21 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: U3G913, 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 47.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: containing 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 7, 2018
RadiationMonochromator: FRE+ / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→45.6 Å / Num. obs: 84912 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.076 / Net I/σ(I): 9.3
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.541 / Rpim(I) all: 0.53 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ziy

3ziy


Resolution: 2.25→42.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.596 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23698 4426 5 %RANDOM
Rwork0.17884 ---
obs0.1817 84912 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.131 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---1.12 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.25→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14615 0 46 1062 15723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01315065
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713824
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.64520474
X-RAY DIFFRACTIONr_angle_other_deg1.2031.56832133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.07551919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40522.701696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26152288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.231561
X-RAY DIFFRACTIONr_chiral_restr0.0590.21890
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023108
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_it0.8692.3227685
X-RAY DIFFRACTIONr_mcbond_other0.8692.3217683
X-RAY DIFFRACTIONr_mcangle_it1.4863.4769597
X-RAY DIFFRACTIONr_mcangle_other1.4853.4769597
X-RAY DIFFRACTIONr_scbond_it0.9992.4577380
X-RAY DIFFRACTIONr_scbond_other12.4587381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7283.62610876
X-RAY DIFFRACTIONr_long_range_B_refined3.52827.24915897
X-RAY DIFFRACTIONr_long_range_B_other3.52927.25215898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 267 -
Rwork0.263 5279 -
obs--79.66 %
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)
10.2098-0.13740.16750.20950.07320.52820.03670.0313-0.031-0.0099-0.01340.02050.00310.0053-0.02330.02840.0089-0.0050.1656-0.01640.00561.75548.35-0.717
20.2060.205-0.10220.29290.05540.3927-0.0321-0.0051-0.0168-0.04820.0144-0.0007-0.0134-0.01030.01770.0092-0.01430.0010.16090.00490.011234.5021.977-37.069
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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