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- PDB-1et5: CRYSTAL STRUCTURE OF NITRITE REDUCTASE ASP98ASN MUTANT FROM ALCAL... -

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Basic information

Entry
Database: PDB / ID: 1et5
TitleCRYSTAL STRUCTURE OF NITRITE REDUCTASE ASP98ASN MUTANT FROM ALCALIGENES FAECALIS S-6
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / Greek key beta barrel domain
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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / 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 speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBoulanger, M.J. / Kukimoto, M. / Nishiyama, M. / Horinouchi, S. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase.
Authors: Boulanger, M.J. / Kukimoto, M. / Nishiyama, M. / Horinouchi, S. / Murphy, M.E.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2000Provider: 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 3, 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_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.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.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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,1365
Polymers36,8781
Non-polymers2584
Water4,828268
1
A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40715
Polymers110,6333
Non-polymers77412
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 area12710 Å2
ΔGint-102 kcal/mol
Surface area33380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.940, 127.940, 66.426
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-504-

ZN

21A-505-

ZN

DetailsBiological assembly is a trimer constructed from chain A by the threefold axis

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Components

#1: Protein NITRITE REDUCTASE / / CU-NIR


Mass: 36877.664 Da / Num. of mol.: 1 / Fragment: 40 - 376 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P38501, EC: 1.7.99.3
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: sodium cacodylate, zinc acetate, PEG 4000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium cacodylate11
210-15 %PEG400011or PEG6000, PEG8000
350-75 mMzinc salt11
410-15 mg/mlprotein11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 92090 / Num. obs: 30437 / Redundancy: 2.9 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.68
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.246 / Num. unique all: 6121
Reflection
*PLUS
% possible obs: 95.2 % / Num. measured all: 92090
Reflection shell
*PLUS
% possible obs: 95.6 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→500 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2222100.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Least squares method
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2763 9.1 %RANDOM
Rwork0.185 ---
obs0.185 30434 95.1 %-
all-31965 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.54 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.01 Å2-1.89 Å20 Å2
2---5.01 Å20 Å2
3---10.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 4 268 2832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 495 9.7 %
Rwork0.248 4600 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 9.1 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.248 / Num. reflection obs: 6121

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