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- PDB-1cnf: STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE O... -

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Entry
Database: PDB / ID: 1cnf
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
ComponentsNITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / NITROGENOUS ACCEPTOR / NITRATE ASSIMILATING ENZYME
Function / homologyImmunoglobulin E-set / NADH:cytochrome b5 reductase-like / Cytochrome b5-like heme/steroid binding domain superfamily / Oxidoreductase, molybdopterin-binding domain superfamily / Cytochrome b5, heme-binding site / Riboflavin synthase-like beta-barrel / FAD-binding domain, ferredoxin reductase-type / Oxidoreductase molybdopterin binding domain / Eukaryotic molybdopterin oxidoreductase / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain ...Immunoglobulin E-set / NADH:cytochrome b5 reductase-like / Cytochrome b5-like heme/steroid binding domain superfamily / Oxidoreductase, molybdopterin-binding domain superfamily / Cytochrome b5, heme-binding site / Riboflavin synthase-like beta-barrel / FAD-binding domain, ferredoxin reductase-type / Oxidoreductase molybdopterin binding domain / Eukaryotic molybdopterin oxidoreductase / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Flavoprotein pyridine nucleotide cytochrome reductase / Cytochrome b5-like Heme/Steroid binding domain / Oxidoreductase FAD/NAD(P)-binding / Cytochrome b5-like heme/steroid binding domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase NAD-binding domain / Oxidoreductase FAD-binding domain / Mo-co oxidoreductase dimerisation domain / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Ferredoxin reductase-type FAD binding domain profile. / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / nitrate reductase (NADH) / nitrate reductase (NADH) activity / molybdenum ion binding / nitrate assimilation / nitric oxide biosynthetic process / FAD binding / heme binding / cytosol / Nitrate reductase [NADH]
Function and homology information
Specimen sourceZea mays (maize)
MethodX-RAY DIFFRACTION / 2.7 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 1, 1995 / Release: Apr 20, 1995
RevisionDateData content typeGroupProviderType
1.0Apr 20, 1995Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8033
Polyers30,5901
Non-polymers1,2132
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MH 3
Atom site foot note1: CIS PROLINE - PRO 115 / 2: CIS PROLINE - PRO 163

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Components

#1: Protein/peptide NITRATE REDUCTASE /


Mass: 30590.322 Da / Num. of mol.: 1 / Source: (gene. exp.) Zea mays (maize) / Genus: Zea / 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 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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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 / Density percent sol: 60.93 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber obs: 8225 / Observed criterion sigma I: 1 / Percent possible obs: 81
Reflection
*PLUS
D resolution high: 2.7 / Number measured all: 20157 / Rmerge I obs: 0.062 / Redundancy: 2.4 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefineSigma F: 1
Displacement parametersB iso mean: 33
Least-squares processR factor R free: 0.272 / R factor R work: 0.186 / R factor obs: 0.186 / Highest resolution: 2.7 / Lowest resolution: 8 / Number reflection obs: 8225
Refine hist #LASTHighest resolution: 2.7 / Lowest resolution: 8
Number of atoms included #LASTProtein: 2074 / Nucleic acid: 0 / Ligand: 80 / Solvent: 0 / Total: 2154
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.2
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
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_deg2.1

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