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- PDB-2cnd: STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE O... -

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Basic information

Entry
Database: PDB / ID: 2cnd
TitleSTRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN
ComponentsNADH-DEPENDENT NITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRATE ASSIMILATING ENZYME / NITROGENOUS ACCEPTOR
Function / homology
Function and homology information


nitrate reductase (NADH) / nitrate reductase (NADH) activity / molybdenum ion binding / nitrate assimilation / nitric oxide biosynthetic process / FAD binding / heme binding
Similarity search - Function
NADH:cytochrome b5 reductase-like / 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 / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. ...NADH:cytochrome b5 reductase-like / 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 / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / 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-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Nitrate reductase [NADH] 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLu, G. / Lindqvist, Y. / Schneider, G.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structural studies on corn nitrate reductase: refined structure of the cytochrome b reductase fragment at 2.5 A, its ADP complex and an active-site mutant and modeling of the cytochrome b domain.
Authors: Lu, G. / Lindqvist, Y. / Schneider, G. / Dwivedi, U. / Campbell, W.
#1: Journal: To be Published
Title: A Method for Processing Diffraction Data from Twinned Crystals and its Application in the Structure Determination of a Fad(Slash)Nadh Binding Fragment of Nitrate Reductase
Authors: Lu, G. / Lindqvist, Y. / Schneider, G.
#2: Journal: Structure / Year: 1995
Title: Crystal Structure of the Fad Containing Fragment of Corn Nitrate Reductase at 2.5 Angstroms Resolution: Relationship to Other Flavoprotein Reductase
Authors: Lu, G. / Campbell, W. / Lindqvist, Y. / Schneider, G.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Crystallographic Studies of the Fad Domain of Corn Nadh:Nitrate Reductase
Authors: Lu, G. / Campbell, W. / Lindqvist, Y. / Schneider, G.
History
DepositionFeb 1, 1995Processing site: BNL
SupersessionApr 20, 1995ID: 1CND
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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

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Assembly

Deposited unit
A: NADH-DEPENDENT NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3762
Polymers30,5901
Non-polymers7861
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.200, 145.200, 47.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Atom site foot note1: CIS PROLINE - PRO 115 / 2: CIS PROLINE - PRO 163

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Components

#1: Protein NADH-DEPENDENT NITRATE REDUCTASE


Mass: 30590.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Organ: LEAF / References: UniProt: P17571, EC: 1.6.6.1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.93 %

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Data collection

ReflectionNum. obs: 10519 / % possible obs: 81 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 5.4 % / Num. measured all: 57374 / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→6.5 Å / σ(F): 1
RfactorNum. reflection
Rfree0.223 -
Rwork0.187 -
obs0.187 9754
Displacement parametersBiso mean: 35 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 53 75 2202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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