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- PDB-4zk8: Copper-containing nitrite reductase from thermophilic bacterium G... -

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Basic information

Entry
Database: PDB / ID: 4zk8
TitleCopper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / Copper / Denitrification / Electron Transfer / Nitrite
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / outer membrane-bounded periplasmic space / 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 / DI(HYDROXYETHYL)ETHER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsFukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science254626 Japan
CitationJournal: J.Biochem. / Year: 2014
Title: Structural insights into the function of a thermostable copper-containing nitrite reductase
Authors: Fukuda, Y. / Tse, K.M. / Lintuluoto, M. / Fukunishi, Y. / Mizohata, E. / Matsumura, H. / Takami, H. / Nojiri, M. / Inoue, T.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 20, 2015ID: 3WKO
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,59930
Polymers35,5231
Non-polymers2,07629
Water6,774376
1
A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,79690
Polymers106,5693
Non-polymers6,22787
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 area19300 Å2
ΔGint-516 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.054, 115.054, 84.417
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-853-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase / / Copper Nitrite Reductase


Mass: 35523.062 Da / Num. of mol.: 1 / Fragment: UNP residues 31-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria)
Strain: NG80-2 / Gene: nirK / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: A4IL26

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Non-polymers , 9 types, 405 molecules

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


Mass: 63.546 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5.5% PEG 4000, 0.1M sodium acetate, 0.075M copper sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 141618 / % possible obs: 95.7 % / Redundancy: 2.6 % / Rsym value: 0.073 / Net I/σ(I): 13.2
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 1.6 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→22.06 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14604 7102 5 %RANDOM
Rwork0.12034 ---
obs0.12162 134511 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.594 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.15→22.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 76 376 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192660
X-RAY DIFFRACTIONr_bond_other_d00.022538
X-RAY DIFFRACTIONr_angle_refined_deg2.3211.9613644
X-RAY DIFFRACTIONr_angle_other_deg3.73635880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0695345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.49625.614114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.866154
X-RAY DIFFRACTIONr_chiral_restr0.1530.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213094
X-RAY DIFFRACTIONr_gen_planes_other0.0270.02588
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_it1.3471.0841314
X-RAY DIFFRACTIONr_mcbond_other1.2531.0731310
X-RAY DIFFRACTIONr_mcangle_it1.5361.6221679
X-RAY DIFFRACTIONr_mcangle_other1.5411.6231680
X-RAY DIFFRACTIONr_scbond_it3.3811.4011346
X-RAY DIFFRACTIONr_scbond_other3.3271.4011346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6131.9961966
X-RAY DIFFRACTIONr_long_range_B_refined4.12111.1643276
X-RAY DIFFRACTIONr_long_range_B_other4.1211.1773277
X-RAY DIFFRACTIONr_rigid_bond_restr12.56235198
X-RAY DIFFRACTIONr_sphericity_free24.9575127
X-RAY DIFFRACTIONr_sphericity_bonded8.11655420
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 514 -
Rwork0.232 9408 -
obs--90.41 %

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