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- PDB-2q49: Ensemble refinement of the protein crystal structure of gene prod... -

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Basic information

Entry
Database: PDB / ID: 2q49
TitleEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g19940
ComponentsProbable N-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / Ensemble Refinement / Refinement Methodology Development / AT2G19940 / CATH 3.40.50 FOLD / SEMIALDEHYDE DEHYDROGENASE FAMILY / TETRAMER / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / chloroplast stroma / chloroplast / NAD binding / protein dimerization activity / copper ion binding / nucleolus
Similarity search - Function
N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 ...N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.19 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable N-acetyl-gamma-glutamyl-phosphate reductase
B: Probable N-acetyl-gamma-glutamyl-phosphate reductase
C: Probable N-acetyl-gamma-glutamyl-phosphate reductase
D: Probable N-acetyl-gamma-glutamyl-phosphate reductase


Theoretical massNumber of molelcules
Total (without water)158,6024
Polymers158,6024
Non-polymers00
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17100 Å2
ΔGint-81 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.597, 107.067, 85.754
Angle α, β, γ (deg.)90.000, 118.880, 90.000
Int Tables number4
Space group name H-MP1211
Number of models8

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Components

#1: Protein
Probable N-acetyl-gamma-glutamyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 39650.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At2g19940, F6F22.3 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2)
References: UniProt: Q93Z70, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XYG.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1XYG

1xyg


Resolution: 2.19→27.31 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 273025 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1xyg and the first data set in the deposited structure factor file for 1xyg ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1xyg and the first data set in the deposited structure factor file for 1xyg along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3240 5.1 %RANDOM
Rwork0.152 ---
obs0.152 63966 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.766 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.68 Å20 Å2-0.99 Å2
2--19.33 Å20 Å2
3----11.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.19→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10720 0 0 956 11676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.19-2.330.2764495.20.21282590.01311453870876
2.33-2.510.2595515.30.19397820.011113991033390.6
2.51-2.760.26254050.166103270.011114461086794.9
2.76-3.160.2295294.80.15106040.01114651113397.1
3.16-3.980.1945945.20.138107520.008114671134698.9
3.98-27.310.18257750.14110020.008116211157999.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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