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- PDB-1ndt: NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS -

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Basic information

Entry
Database: PDB / ID: 1ndt
TitleNITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
ComponentsPROTEIN (NITRITE REDUCTASE)
KeywordsOXIDOREDUCTASE / NITRITE REDUCTASE / BLUE COPPER
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 / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDodd, F.E. / Vanbeeumen, J. / Eady, R.R. / Hasnain, S.S.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner.
Authors: Dodd, F.E. / Van Beeumen, J. / Eady, R.R. / Hasnain, S.S.
History
DepositionOct 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / 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_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: PROTEIN (NITRITE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2084
Polymers36,0461
Non-polymers1633
Water2,954164
1
A: PROTEIN (NITRITE REDUCTASE)
hetero molecules

A: PROTEIN (NITRITE REDUCTASE)
hetero molecules

A: PROTEIN (NITRITE REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,62512
Polymers108,1373
Non-polymers4889
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area14030 Å2
ΔGint-130 kcal/mol
Surface area33320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.236, 81.236, 100.034
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PROTEIN (NITRITE REDUCTASE)


Mass: 36045.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COPPER, CHLORIDE / Source: (natural) Achromobacter xylosoxidans (bacteria) / Cellular location: PERIPLASM / Strain: XYLOSOXIDANS / References: UniProt: O68601, 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTYPE 1 COPPER CENTER TYPE II COPPER CENTER TYPE II COPPER BOUND CHLORIDE
Sequence detailsthe gene sequence was performed independently and is referenced in the journal citation: "The blue ...the gene sequence was performed independently and is referenced in the journal citation: "The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme" M.Prudencio,R.R.Eady,G.Sawers J Bacteriol. 1999 Apr;181(8):2323-2329.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 59 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG40001reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium acetate1reservoir
410 mg/mlprotein1drop
520 mMMES1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1996 / Details: TORROIDAL MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→70.4 Å / Num. obs: 21904 / % possible obs: 98.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 135597
Reflection shell
*PLUS
% possible obs: 99.3 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFN MONOMER

1afn
PDB Unreleased entry


Resolution: 2.1→20 Å / SU B: 4.32 / SU ML: 0.11 / Cross valid method: THROUGHOUT, EXCEPT FINAL CYCLE / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1099 5 %RANDOM
Rwork0.167 ---
obs0.164 20483 99.7 %-
Displacement parametersBiso mean: 19.9 Å2 / Baniso 23: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 3 164 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it3
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_singtor_nbd0.3
X-RAY DIFFRACTIONp_multtor_nbd0.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.3
X-RAY DIFFRACTIONp_planar_tor7
X-RAY DIFFRACTIONp_staggered_tor15
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25
X-RAY DIFFRACTIONp_special_tor15

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