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- PDB-2q4b: Ensemble refinement of the protein crystal structure of selenomet... -

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Basic information

Entry
Database: PDB / ID: 2q4b
TitleEnsemble refinement of the protein crystal structure of selenomethionyl gene product from Arabidopsis thaliana At5g02240 in space group P21212
ComponentsProtein At5g02240
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / NADP / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


response to abscisic acid / apoplast / plant-type vacuole / chloroplast stroma / oxidoreductase activity / plasma membrane / cytosol
Similarity search - Function
Sanguinarine reductase SARED1-like / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein At5g02240
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.096 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 1.1Sep 25, 2007Group: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Protein At5g02240
B: Protein At5g02240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6724
Polymers54,1862
Non-polymers1,4872
Water6,648369
1
A: Protein At5g02240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8362
Polymers27,0931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein At5g02240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8362
Polymers27,0931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.634, 77.286, 92.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Number of models16

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Components

#1: Protein Protein At5g02240


Mass: 27092.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At5g02240, T7H20_290 / Plasmid: pvp-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q94EG6
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.5 Å3/Da / Density % sol: 49.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1YBM.

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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 1YBM

1ybm


Resolution: 2.096→29.087 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1844723.5 / 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 1ybm and the first data set in the deposited structure factor file for 1ybm ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ybm and the first data set in the deposited structure factor file for 1ybm along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 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
Rfree0.257 1519 5.1 %RANDOM
Rwork0.18 ---
obs0.18 29771 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.682 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.096→29.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 96 369 4137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_angle_deg2.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d2.19
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.652
X-RAY DIFFRACTIONc_scangle_it3.92.5
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 (%)
2.096-2.230.3172344.90.23945200.0215259475490.4
2.23-2.40.2992414.80.20948180.0195294505995.6
2.4-2.650.2872605.20.19547560.0185264501695.3
2.65-3.030.2892675.30.19247390.0185310500694.3
3.03-3.810.2732615.20.18947350.0175363499693.2
3.81-29.090.2062565.20.14946840.0135579494088.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3nap_xplor_par.txt

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