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- PDB-2q3t: Ensemble refinement of the protein crystal structure of gene prod... -

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Basic information

Entry
Database: PDB / ID: 2q3t
TitleEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680
ComponentsProtein At3g22680
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


gene silencing by siRNA-directed DNA methylation / RNA polymerase V complex / : / : / siRNA processing / : / DNA binding / nucleoplasm / nucleus
Similarity search - Function
RDM1 protein domain / Protein RDM1, plant / RDM1 superfamily / RNA-directed DNA methylation 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 1.6 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: Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana
Authors: Allard, S.T.M. / Bingman, C.A. / Johnson, K.A. / Wesenberg, G.E. / Bitto, E. / Jeon, W.B. / Phillips Jr., G.N.
History
DepositionMay 30, 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: Derived calculations / 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein At3g22680
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1549
Polymers18,0031
Non-polymers1,1518
Water3,099172
1
A: Protein At3g22680
hetero molecules

A: Protein At3g22680
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30918
Polymers36,0062
Non-polymers2,30316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5850 Å2
ΔGint-92 kcal/mol
Surface area13670 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.450, 83.450, 60.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Number of models16

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Components

#1: Protein Protein At3g22680


Mass: 18003.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At3g22680, MWI23.5 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9LUJ3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.38 Å3/Da / Density % sol: 63.61 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1VK5.

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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 1VK5

1vk5


Resolution: 1.6→31.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1199955.5 / 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 1vk5 and the first data set in the deposited structure factor file for 1vk5 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vk5 and the first data set in the deposited structure factor file for 1vk5 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
Rfree0.17 1633 5.1 %RANDOM
Rwork0.139 ---
obs0.139 32203 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.432 Å2 / ksol: 0.421 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 63 172 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.125
X-RAY DIFFRACTIONc_angle_deg7.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d5.33
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.312.5
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 (%)
1.6-1.70.192865.40.15649970.0115299528399.7
1.7-1.840.1562845.30.11250290.0095325531399.8
1.84-2.020.1632755.20.10450640.015343533999.9
2.02-2.310.1452805.20.11950550.00953355335100
2.31-2.910.152424.50.11851290.0153715371100
2.91-31.030.1912664.80.16952960.01255645562100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cps_xplor_par.txt
X-RAY DIFFRACTION5edo.param

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