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- PDB-5ytl: Crystal structure of Geobacillus thermodenitrificans copper-conta... -

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Basic information

Entry
Database: PDB / ID: 5ytl
TitleCrystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper / nitrite reductase
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
ACETIC ACID / COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsFukuda, Y. / Matsusaki, T. / Tse, K.M. / Mizohata, E. / Murphy, M.E.P. / Inoue, T.
Funding support Japan, Canada, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
The Natural Sciences and Engineering Research Council of Canada Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Authors: Fukuda, Y. / Matsusaki, T. / Tse, K.M. / Mizohata, E. / Murphy, M.E.P. / Inoue, T.
History
DepositionNov 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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.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

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1379
Polymers35,5231
Non-polymers6148
Water5,531307
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)108,41227
Polymers106,5693
Non-polymers1,84224
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 area11230 Å2
ΔGint-122 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.314, 115.314, 84.534
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-404-

CU

21A-788-

HOH

31A-801-

HOH

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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) / Strain (production host): BL21(DE3)
References: UniProt: A0A1W6VP04, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 315 molecules

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


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: 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
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M acetate buffer pH 4.5, 6.0 % PEG 4000, 75mM CuSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 81993 / % possible obs: 99.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 22.5 Å2 / Rrim(I) all: 0.072 / Net I/σ(I): 21.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4135 / CC1/2: 0.723 / Rrim(I) all: 0.558 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.401→26.321 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 11.78
RfactorNum. reflection% reflection
Rfree0.1397 4050 4.94 %
Rwork0.1132 --
obs0.1145 81973 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.401→26.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 25 307 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052521
X-RAY DIFFRACTIONf_angle_d0.8843458
X-RAY DIFFRACTIONf_dihedral_angle_d18.152936
X-RAY DIFFRACTIONf_chiral_restr0.088377
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4009-1.41730.21961570.19622686X-RAY DIFFRACTION99
1.4173-1.43460.24471270.18912697X-RAY DIFFRACTION100
1.4346-1.45280.19671400.17762733X-RAY DIFFRACTION100
1.4528-1.47190.19461400.16222679X-RAY DIFFRACTION100
1.4719-1.49210.15741390.14972668X-RAY DIFFRACTION100
1.4921-1.51340.1651220.14212743X-RAY DIFFRACTION100
1.5134-1.5360.18371680.13832695X-RAY DIFFRACTION100
1.536-1.560.14791410.12882697X-RAY DIFFRACTION100
1.56-1.58550.15521430.11532667X-RAY DIFFRACTION100
1.5855-1.61290.15771450.11332700X-RAY DIFFRACTION100
1.6129-1.64220.16091600.10582696X-RAY DIFFRACTION100
1.6422-1.67380.13061510.10122690X-RAY DIFFRACTION100
1.6738-1.70790.11881390.09312679X-RAY DIFFRACTION100
1.7079-1.74510.13451450.09132734X-RAY DIFFRACTION100
1.7451-1.78570.131260.08832683X-RAY DIFFRACTION100
1.7857-1.83030.1181460.08952684X-RAY DIFFRACTION100
1.8303-1.87980.11911160.08832734X-RAY DIFFRACTION100
1.8798-1.93510.11551290.08752692X-RAY DIFFRACTION100
1.9351-1.99750.10591310.09242716X-RAY DIFFRACTION100
1.9975-2.06890.10981230.09462725X-RAY DIFFRACTION100
2.0689-2.15170.12051420.09552653X-RAY DIFFRACTION100
2.1517-2.24950.14271500.10182672X-RAY DIFFRACTION99
2.2495-2.36810.12921170.10862699X-RAY DIFFRACTION99
2.3681-2.51630.14071410.11542701X-RAY DIFFRACTION99
2.5163-2.71040.14831320.1272662X-RAY DIFFRACTION99
2.7104-2.98290.16861610.12442680X-RAY DIFFRACTION99
2.9829-3.41370.13691110.11382668X-RAY DIFFRACTION98
3.4137-4.29790.1191610.10722614X-RAY DIFFRACTION98
4.2979-26.32540.14821470.12572576X-RAY DIFFRACTION95

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