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- PDB-5ocb: Crystal structure of nitric oxide bound D97N mutant of three-doma... -

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Basic information

Entry
Database: PDB / ID: 5ocb
TitleCrystal structure of nitric oxide bound D97N mutant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii
ComponentsNitrite reductase, copper-containing
KeywordsELECTRON TRANSPORT / nitrite reductase / electron transfer / redox reactions / tyrosine activation
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 / NITRIC OXIDE / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRalstonia sp. 5_2_56FAA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsDong, J. / Sasaki, D. / Eady, R. / Antonyuk, S.V. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006960/1 United Kingdom
CitationJournal: To be published
Title: Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases
Authors: Dong, J. / Sasaki, D. / Eady, R. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 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_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_ptnr1_label_alt_id / _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

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Assembly

Deposited unit
A: Nitrite reductase, copper-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7235
Polymers49,9481
Non-polymers7764
Water12,070670
1
A: Nitrite reductase, copper-containing
hetero molecules

A: Nitrite reductase, copper-containing
hetero molecules

A: Nitrite reductase, copper-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,16915
Polymers149,8433
Non-polymers2,32712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18520 Å2
ΔGint-211 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.460, 180.460, 180.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-197-

ARG

21A-1237-

HOH

31A-1251-

HOH

41A-1260-

HOH

51A-1269-

HOH

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Components

#1: Protein Nitrite reductase, copper-containing


Mass: 49947.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. 5_2_56FAA (bacteria) / Gene: HMPREF0989_00586 / Plasmid: PET26B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: U3G913
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 4.36 Å3/Da / Density % sol: 72 % / Description: red cubes
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M SODIUM CITRATE, 20 mM BIS-TRIS-PROPANE-HCL PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2016 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.78→90.23 Å / Num. obs: 91145 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.056 / Net I/σ(I): 8
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 13378 / CC1/2: 0.504 / Rpim(I) all: 0.424 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OCF

5ocf


Resolution: 1.78→30.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.824 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 2743 3 %RANDOM
Rwork0.14361 ---
obs0.14416 88375 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.629 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.78→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 47 670 4145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193832
X-RAY DIFFRACTIONr_bond_other_d0.0020.023636
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9765269
X-RAY DIFFRACTIONr_angle_other_deg0.95438411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44424.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80715601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2351519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214490
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02881
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_it1.5182.3031927
X-RAY DIFFRACTIONr_mcbond_other1.5132.3021925
X-RAY DIFFRACTIONr_mcangle_it2.2733.442422
X-RAY DIFFRACTIONr_mcangle_other2.2753.4432423
X-RAY DIFFRACTIONr_scbond_it2.0642.4981905
X-RAY DIFFRACTIONr_scbond_other2.0642.4971903
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1533.6732818
X-RAY DIFFRACTIONr_long_range_B_refined7.91821.3084841
X-RAY DIFFRACTIONr_long_range_B_other6.22119.3084368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 198 -
Rwork0.283 6583 -
obs--99.15 %

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