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- PDB-3wkp: C135A mutant of Geobacillus thermodenitrificans copper-containing... -

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Basic information

Entry
Database: PDB / ID: 3wkp
TitleC135A mutant of Geobacillus thermodenitrificans copper-containing nitrite reductase in complex with nitrite
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / Greek Key Beta Barrel / nitrite reductase
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
COPPER (II) ION / NITRITE ION / DI(HYDROXYETHYL)ETHER / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsFukuda, Y. / Inoue, T.
CitationJournal: to be published
Title: C135A mutant of Geobacillus thermodenitrificans copper-containing nitrite reductase in complex with nitrite
Authors: Fukuda, Y. / Inoue, T.
History
DepositionOct 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 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 / 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_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_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.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)36,0158
Polymers35,4911
Non-polymers5247
Water4,252236
1
A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules

A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,04624
Polymers106,4733
Non-polymers1,57321
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 area11280 Å2
ΔGint-129 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.866, 114.866, 84.039
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-698-

HOH

21A-733-

HOH

31A-734-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase / / copper-containing nitrite reductase


Mass: 35490.996 Da / Num. of mol.: 1 / Fragment: UNP residues 31-352 / Mutation: C135A
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 , 5 types, 243 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
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, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.901→50 Å / Num. all: 30251 / Num. obs: 30251 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 2.3 %
Reflection shellResolution: 1.901→1.94 Å / Redundancy: 2 % / Num. unique all: 1461 / % possible all: 90.7

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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 / Resolution: 1.901→25.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.654 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1527 5 %RANDOM
Rwork0.15644 ---
all0.15891 28714 --
obs0.15889 28714 92.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.578 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.901→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 22 236 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022451
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.9473344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2015310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.33425.421107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.326154
X-RAY DIFFRACTIONr_chiral_restr0.1590.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211889
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 89 -
Rwork0.208 2014 -
obs--87.55 %

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