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- PDB-2q40: Ensemble refinement of the protein crystal structure of gene prod... -

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Basic information

Entry
Database: PDB / ID: 2q40
TitleEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g17340
ComponentsProtein At2g17340
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / AT2G17340 / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / coenzyme A biosynthetic process / hydrolase activity / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
AF1104-like / Damage-control phosphatase At2g17340 / At2g17340, three-helix bundle domain / AF1104-like / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Type II pantothenate kinase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Damage-control phosphatase At2g17340
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 1.7 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The structure at 1.7A resolution of the protein product of the At2g17340 gene from Arabidopsis thaliana
Authors: Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Protein At2g17340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9053
Polymers40,8561
Non-polymers492
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.174, 43.280, 52.644
Angle α, β, γ (deg.)74.570, 74.600, 84.040
Int Tables number1
Space group name H-MP1
Number of models16

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Components

#1: Protein Protein At2g17340


Mass: 40856.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At2g17340, F5J6.10 / Plasmid details: pQE derivative / Plasmid: pVP13-GW / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta, B834-DE3 pLacI+RARE / References: UniProt: Q949P3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.08 Å3/Da / Density % sol: 40.86 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XFI.

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Data collection

DetectorType: APS-1
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 1XFI

1xfi


Resolution: 1.7→34.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 758638.5 / 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 1xfi and the first data set in the deposited structure factor file for 1xfi ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1xfi and the first data set in the deposited structure factor file for 1xfi 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
Rfree0.221 1763 5 %RANDOM
Rwork0.165 ---
obs0.165 35192 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.77 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 2 357 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.882.5
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 (%)
1.7-1.810.3382684.70.2553930.0216084566193
1.81-1.950.2662614.50.17755640.0166034582596.5
1.95-2.140.2273015.10.15655670.0136044586897.1
2.14-2.450.22829750.15455980.0136031589597.7
2.45-3.090.2153255.40.15756620.0126082598798.4
3.09-34.910.2033115.20.16456450.0126019595699
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param

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