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- PDB-1p90: The Three-dimensional Structure of the Core Domain of NafY from A... -

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Basic information

Entry
Database: PDB / ID: 1p90
TitleThe Three-dimensional Structure of the Core Domain of NafY from Azotobacter vinelandii determined at 1.8 resolution
Componentshypothetical protein
KeywordsPROTEIN BINDING / Ribonuclease H motif
Function / homology
Function and homology information


metal cluster binding / nitrogen fixation
Similarity search - Function
Nitrogen fixation protein NifX / Dinitrogenase iron-molybdenum cofactor, N-terminal / NifX-like domain / Dinitrogenase iron-molybdenum cofactor, N-terminal domain superfamily / Dinitrogenase iron-molybdenum cofactor, N-terminal / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 ...Nitrogen fixation protein NifX / Dinitrogenase iron-molybdenum cofactor, N-terminal / NifX-like domain / Dinitrogenase iron-molybdenum cofactor, N-terminal domain superfamily / Dinitrogenase iron-molybdenum cofactor, N-terminal / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrogenase gamma subunit
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsDyer, D.H. / Rubio, L.M. / Thoden, J.B. / Holden, H.M. / Ludden, P.W. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Three-dimensional Structure of the Core Domain of NafY from Azotobacter vinelandii determined at 1.8 A resolution
Authors: Dyer, D.H. / Rubio, L.M. / Thoden, J.B. / Holden, H.M. / Ludden, P.W. / Rayment, I.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5772
Polymers15,5151
Non-polymers621
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 49.200, 99.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

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Components

#1: Protein hypothetical protein / NafY protein


Mass: 15514.565 Da / Num. of mol.: 1 / Fragment: core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: NafY / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F5X9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3 ml of NafY protein at 10 mg/ml combined with an equal volume of 13% PEG 10000, 2.5% glycerol, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
213 %PEG100001reservoir
32.5 %glycerol1reservoir
4100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 24908 / Num. obs: 24908 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2531 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % possible obs: 100 %
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 100 % / Num. unique obs: 2531

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
TNTrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1347 -random 10%
Rwork0.188 ---
all0.194 13182 --
obs0.188 13182 100 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 4 174 1110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.47
X-RAY DIFFRACTIONt_dihedral_angle_d0.005
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 11853 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.7

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