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- PDB-3wni: 1.50 A resolution crystal structure of dioxygen bound copper-cont... -

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Basic information

Entry
Database: PDB / ID: 3wni
Title1.50 A resolution crystal structure of dioxygen bound copper-containing nitrite reductase from Geobacillus thermodenitrificans
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / Greek key beta barrel / dissimilatory nitrite reductase / periplasm-like space
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, C-terminal / Multicopper oxidase / 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, C-terminal / Multicopper oxidase / 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 / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFukuda, Y. / Inoue, T.
CitationJournal: To be Published
Title: Crystallographic evidence for side-on dioxygen trapped on type 2 copper in copper-containing nitrite reductase
Authors: Fukuda, Y. / Inoue, T.
History
DepositionDec 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,0308
Polymers35,5231
Non-polymers5077
Water6,179343
1
A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,09024
Polymers106,5693
Non-polymers1,52121
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 area11140 Å2
ΔGint-112 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.017, 115.017, 84.543
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-694-

HOH

21A-824-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 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 (bacteria)
Strain: NG80-2 / Gene: nirK / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IL26

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Non-polymers , 6 types, 350 molecules

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


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, 5.5%(w/v) PEG 4000, 0.075M CuSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.75 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 64781 / Num. obs: 64781 / % possible obs: 97 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.89 / Num. unique all: 6639 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKO

3wko
PDB Unreleased entry


Resolution: 1.5→42.91 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.684 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.14859 3293 5.1 %RANDOM
Rwork0.10755 ---
all0.10963 61473 --
obs0.10963 61473 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.714 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 24 343 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1981.9533476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2065328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.27825.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80615422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.52154
X-RAY DIFFRACTIONr_chiral_restr0.1670.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0221989
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.5132543
X-RAY DIFFRACTIONr_sphericity_free36.2415123
X-RAY DIFFRACTIONr_sphericity_bonded13.59152726
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 251 -
Rwork0.137 4662 -
obs--99.43 %

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