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- PDB-6l46: High-resolution neutron and X-ray joint refined structure of copp... -

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Basic information

Entry
Database: PDB / ID: 6l46
TitleHigh-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper / nitrite reductase / neutron
Function / homology
Function and homology information


: / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / DEUTERATED WATER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsFukuda, Y. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.
Authors: Fukuda, Y. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.
History
DepositionOct 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)35,9548
Polymers35,5231
Non-polymers4317
Water8,251458
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)107,86224
Polymers106,5693
Non-polymers1,29221
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 area11550 Å2
ΔGint-227 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.212, 114.212, 83.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Components on special symmetry positions
IDModelComponents
11A-947-

DOD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper-containing nitrite reductase


Mass: 35523.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: nirK, GTHT12_00198 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1W6VP04, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 465 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: D2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M acetate buffer pH 4.6, 5.5% (w/v) PEG 4000, and 50 mM CuSO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.15-4.89
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELDec 16, 2018
iBIX2DIFFRACTOMETERNov 26, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.151
34.891
Reflection

Entry-ID: 6L46

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)Biso Wilson estimate (Å2)
1.03-42.5820125199.99.60.0650.021121.2
1.5-17.386499799.76.60.230.09729.56.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.03-1.057.10.6413.598870.9070.253198.7
1.5-1.595.30.6082.294950.7820.285299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
STARGazerdata reduction
Refinement

SU ML: 0.0616 / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 10.3815 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4YSO

4yso

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDCross valid methodσ(F)
1.3-34.13X-RAY DIFFRACTION15.480.11170.09730.097825161001272.511001THROUGHOUT2
1.5-17.071NEUTRON DIFFRACTION0.15860.14160.14212006649643.0999.692FREE R-VALUE
Refinement stepCycle: LAST / Resolution: 1.3→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 14 458 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085648
X-RAY DIFFRACTIONf_angle_d1.05359476
X-RAY DIFFRACTIONf_chiral_restr0.0904383
X-RAY DIFFRACTIONf_plane_restr0.0075898
X-RAY DIFFRACTIONf_dihedral_angle_d21.03911444
NEUTRON DIFFRACTIONf_bond_d0.0085648
NEUTRON DIFFRACTIONf_angle_d1.05359476
NEUTRON DIFFRACTIONf_chiral_restr0.0904383
NEUTRON DIFFRACTIONf_plane_restr0.0075898
NEUTRON DIFFRACTIONf_dihedral_angle_d21.03911444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.1377810.09715480X-RAY DIFFRACTION100
1.32-1.350.1241800.09465485X-RAY DIFFRACTION100
1.35-1.380.099810.09475462X-RAY DIFFRACTION100
1.38-1.410.1366820.09215493X-RAY DIFFRACTION99.98
1.41-1.450.1021790.09265464X-RAY DIFFRACTION100
1.45-1.490.1011820.09035519X-RAY DIFFRACTION100
1.49-1.530.11421400.08785365X-RAY DIFFRACTION100
1.53-1.580.10681750.08815423X-RAY DIFFRACTION100
1.58-1.640.10691690.08685381X-RAY DIFFRACTION100
1.64-1.70.10071740.08965431X-RAY DIFFRACTION100
1.7-1.780.08931680.09125357X-RAY DIFFRACTION100
1.78-1.870.12021740.09745407X-RAY DIFFRACTION100
1.87-1.990.13421690.10485400X-RAY DIFFRACTION100
1.99-2.150.11521720.10065374X-RAY DIFFRACTION100
2.15-2.360.09881760.0925381X-RAY DIFFRACTION100
2.36-2.70.111760.0965406X-RAY DIFFRACTION100
2.7-3.410.10861710.09995388X-RAY DIFFRACTION100
3.41-34.10.12081670.11135395X-RAY DIFFRACTION99.93
1.5-1.540.2241400.19084484NEUTRON DIFFRACTION99
1.5375-1.5790.19691450.1764491NEUTRON DIFFRACTION100
1.579-1.62550.17581440.16894522NEUTRON DIFFRACTION100
1.6255-1.67790.17151430.1564480NEUTRON DIFFRACTION100
1.6779-1.73780.17961410.14694500NEUTRON DIFFRACTION100
1.7378-1.80730.18731430.14584485NEUTRON DIFFRACTION100
1.8073-1.88950.15281450.13754563NEUTRON DIFFRACTION100
1.8895-1.98890.16541420.12854494NEUTRON DIFFRACTION100
1.9889-2.11330.1331440.11244528NEUTRON DIFFRACTION100
2.1133-2.27620.1221480.11044494NEUTRON DIFFRACTION100
2.2762-2.50460.13391440.11024494NEUTRON DIFFRACTION100
2.5046-2.86550.14761450.1274522NEUTRON DIFFRACTION100
2.8655-3.60460.14151440.13314505NEUTRON DIFFRACTION100
3.6046-17.070.14451380.15844391NEUTRON DIFFRACTION97

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