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- PDB-6gt0: Nitrite-bound copper nitrite reductase from Achromobacter cyclocl... -

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Basic information

Entry
Database: PDB / ID: 6gt0
TitleNitrite-bound copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / FEMTOSECOND / SF-ROX / 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
COPPER (II) ION / MALONATE ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 1.5 Å
AuthorsHalsted, T.P. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Eady, R.R. / Antonyuk, S.V. / Yamamoto, M. / Hasnain, S.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R000220/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L006960/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N013972/1 United Kingdom
CitationJournal: Iucrj / Year: 2019
Title: Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography.
Authors: Halsted, T.P. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Blakeley, M.P. / Eady, R.R. / Antonyuk, S.V. / Yamamoto, M. / Hasnain, S.S.
History
DepositionJun 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
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_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)41,3948
Polymers40,8191
Non-polymers5757
Water7,116395
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)124,18324
Polymers122,4583
Non-polymers1,72621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area16250 Å2
ΔGint-104 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.920, 94.920, 94.920
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-743-

HOH

21A-979-

HOH

31A-989-

HOH

41A-993-

HOH

51A-994-

HOH

61A-995-

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: 40819.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 402 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.242 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.242 Å / Relative weight: 1
ReflectionResolution: 1.5→54.86 Å / Num. obs: 45846 / % possible obs: 100 % / Redundancy: 154.7 % / Biso Wilson estimate: 22.6 Å2 / R split: 0.106 / Net I/σ(I): 6.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 50.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2275 / R split: 0.853 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / Pulse energy: 437.7 µJ / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetMotion control: SACLA goniometer
Sample holding: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)
Sample solvent: 3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2.
Support base: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)
Serial crystallography data reductionCrystal hits: 1257 / Frames indexed: 1039 / Frames total: 1257

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Processing

Software
NameVersionClassification
CrystFEL0.6.3data reduction
REFMAC5.8.0230refinement
RefinementResolution: 1.5→54.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.341 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17053 2295 5 %RANDOM
Rwork0.14343 ---
obs0.14481 43498 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 31 395 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0142707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172383
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6723673
X-RAY DIFFRACTIONr_angle_other_deg1.0531.645578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.2155.342351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83123.106132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80915403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7821512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
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_it1.2891.7171339
X-RAY DIFFRACTIONr_mcbond_other1.2871.7151338
X-RAY DIFFRACTIONr_mcangle_it1.8522.5731674
X-RAY DIFFRACTIONr_mcangle_other1.8512.5761675
X-RAY DIFFRACTIONr_scbond_it2.5241.9781368
X-RAY DIFFRACTIONr_scbond_other2.4721.9761366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5842.8641995
X-RAY DIFFRACTIONr_long_range_B_refined4.66621.8082973
X-RAY DIFFRACTIONr_long_range_B_other4.32320.9532868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 171 -
Rwork0.287 3189 -
obs--100 %

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