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- PDB-2bii: crystal structure of nitrate-reducing fragment of assimilatory ni... -

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Basic information

Entry
Database: PDB / ID: 2bii
Titlecrystal structure of nitrate-reducing fragment of assimilatory nitrate reductase from Pichia angusta
ComponentsNITRATE REDUCTASE [NADPH]
KeywordsOXIDOREDUCTASE / FAD / FLAVOPROTEIN / HEME / MOLYBDENUM / NADP / NITRATE ASSIMILATION
Function / homology
Function and homology information


nitrate reductase (NADPH) / nitrate reductase (NADPH) activity / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / nitrate assimilation / nitric oxide biosynthetic process / FAD binding / heme binding
Similarity search - Function
Nitrate reductase NADH dependent / Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily ...Nitrate reductase NADH dependent / Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV) / Nitrate reductase [NADPH]
Similarity search - Component
Biological speciesPICHIA ANGUSTA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G.
CitationJournal: Plant Cell / Year: 2005
Title: Structural Basis of Eukaryotic Nitrate Reduction: Crystal Structures of the Nitrate Reductase Active Site
Authors: Fischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G.
History
DepositionJan 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRATE REDUCTASE [NADPH]
B: NITRATE REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,24017
Polymers97,1292
Non-polymers2,11115
Water14,322795
1
A: NITRATE REDUCTASE [NADPH]
hetero molecules

A: NITRATE REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,14816
Polymers97,1292
Non-polymers2,01914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
MethodPQS
2
B: NITRATE REDUCTASE [NADPH]
hetero molecules

B: NITRATE REDUCTASE [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33218
Polymers97,1292
Non-polymers2,20316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)122.722, 123.080, 149.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2319-

HOH

21B-2320-

HOH

31B-2321-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRATE REDUCTASE [NADPH] / ASSIMILATORY NITRATE REDUCTASE


Mass: 48564.398 Da / Num. of mol.: 2
Fragment: MOCO-BINDING DOMAIN, DIMERIZATION DOMAIN, RESIDUES 1-13,20-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PICHIA ANGUSTA (fungus) / Plasmid: SNAR1-PPICZB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): Y-11430 / References: UniProt: P49050, EC: 1.7.1.2

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Non-polymers , 5 types, 810 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MTV / (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)


Mass: 518.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9MoN5O8PS2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE ...THE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE DATABASE ANNOTATION, SINCE IN THIS STRUCTURE, NO SIDE CHAIN DENSITY FOR AN ARGININE COULD BE OBSERVED. THE N-TERMINAL SEQUENCING OF THE PROTEIN CRYSTAL CONFIRMS THAT THE SEQUENCE BEGINS AT RESIDUE 61. RESIDUES 479-484 ARE NOT VISIBLE IN THIS CRYSTAL STRUCTURE.

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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: 2.9 Å3/Da / Density % sol: 57.3 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2003 / Details: MIRRORS
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 2235039 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIH

2bih


Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.529 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6133 5 %RANDOM
Rwork0.185 ---
obs0.186 116173 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 118 795 7617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9599496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4523.354328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.031151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7121556
X-RAY DIFFRACTIONr_chiral_restr0.1320.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.025352
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23225
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.54123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55826661
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5933241
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9284.52835
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 457
Rwork0.253 8591

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