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- PDB-1kcb: Crystal Structure of a NO-forming Nitrite Reductase Mutant: an An... -

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Basic information

Entry
Database: PDB / ID: 1kcb
TitleCrystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction
ComponentsNitrite Reductase
KeywordsOXIDOREDUCTASE / copper-containing nitrite reductase / BETA BARREL
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsLiu, S.Q. / Chang, T. / Liu, M.Y. / LeGall, J. / Chang, W.C. / Zhang, J.P. / Liang, D.C. / Chang, W.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal structure of a NO-forming nitrite reductase mutant: an analog of a transition state in enzymatic reaction
Authors: Liu, S.Q. / Chang, T. / Liu, M.Y. / LeGall, J. / Chang, W.C. / Zhang, J.P. / Liang, D.C. / Chang, W.R.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrite Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2033
Polymers37,0761
Non-polymers1272
Water3,009167
1
A: Nitrite Reductase
hetero molecules

A: Nitrite Reductase
hetero molecules

A: Nitrite Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6099
Polymers111,2273
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12860 Å2
ΔGint-97 kcal/mol
Surface area33380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.16, 98.16, 98.16
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21A-501-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: y, z, x and z, x, y

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Components

#1: Protein Nitrite Reductase / CU-NIR


Mass: 37075.766 Da / Num. of mol.: 1 / Mutation: I257E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P25006, EC: 1.7.99.3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.05 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulfate, Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
20.1 Mphosphate1reservoirpH4.0
333 %satammonium sulfate1reservoir
45 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 37951 / Num. obs: 37951 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 48.2
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 37954 / % possible obs: 99.9 % / Num. measured all: 393521
Reflection shell
*PLUS
Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NIE

1nie


Resolution: 1.65→9.97 Å / σ(F): 4 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3270 10 %RANDOM
Rwork0.17 ---
all-37951 --
obs-32700 86.1 %-
Refinement stepCycle: LAST / Resolution: 1.65→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 2 167 2745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.52
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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