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- PDB-3gan: Crystal structure of gene product from Arabidopsis thaliana At3g2... -

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Basic information

Entry
Database: PDB / ID: 3gan
TitleCrystal structure of gene product from Arabidopsis thaliana At3g22680 with bound suramin
ComponentsUncharacterized protein At3g22680
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / suramin / Structural Genomics Functional Follow-Up Study / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / 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
Chem-SVR / Protein RDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBurgie, E.S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal structure of gene product from Arabidopsis thaliana At3g22680 with bound suramin
Authors: Burgie, E.S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein At3g22680
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8684
Polymers18,2381
Non-polymers2,6303
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein At3g22680
hetero molecules

A: Uncharacterized protein At3g22680
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7358
Polymers36,4752
Non-polymers5,2606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2100 Å2
ΔGint-14.9 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.381, 58.381, 90.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized protein At3g22680


Mass: 18237.625 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, At3g22680.1, MWI23.5, Q9LUJ3, Y3268_ARATH / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9LUJ3
#2: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/ml MSE Protein, 0.10 M NaCl, 0.0003 M TCEP, 0.010 M Suramin sodium salt, 0.01 M Hepes pH 7.0) mixed in a 1:1 ratio with the Well solution (1.1 M Sodium chloride, 1% ...Details: Protein solution (10 mg/ml MSE Protein, 0.10 M NaCl, 0.0003 M TCEP, 0.010 M Suramin sodium salt, 0.01 M Hepes pH 7.0) mixed in a 1:1 ratio with the Well solution (1.1 M Sodium chloride, 1% DMSO, 0.10 M BTP pH 7.0). Cryoprotected with 20% Ethylene glycol, 1.8 M Sodium chloride, 1% DMSO, 0.10 M BTP pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12503 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.09 / Χ2: 1.371 / Net I/σ(I): 19.77
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.076.20.4582.46911991.04798.7
2.07-2.157.10.34112391.113100
2.15-2.257.30.26812151.175100
2.25-2.377.30.20912241.036100
2.37-2.527.30.15412671.19100
2.52-2.717.30.13212161.244100
2.71-2.997.30.10612511.312100
2.99-3.427.30.0812661.509100
3.42-4.317.20.06912671.626100
4.31-506.70.06313592.38199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.458 / Cor.coef. Fo:Fc: 0.513
Highest resolutionLowest resolution
Rotation3 Å44.11 Å
Translation3 Å44.11 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 12461
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.09-10030.80.554504
4.77-6.0934.70.847508
4.13-4.7725.40.912510
3.74-4.1330.60.91507
3.46-3.7431.20.884505
3.24-3.4631.30.889516
3.08-3.2433.80.885506
2.94-3.08360.851509
2.82-2.9435.20.882525
2.72-2.8239.30.882505
2.63-2.7237.80.862525
2.55-2.6334.90.855519
2.48-2.5534.80.882522
2.42-2.4836.30.876508
2.36-2.4236.50.873544
2.31-2.3638.40.878524
2.26-2.3136.10.891553
2.21-2.2635.40.879559
2.16-2.21360.886573
2.12-2.16370.894587
2.08-2.1239.30.885578
2.05-2.0840.70.85629
2-2.0544.50.841745

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM5phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VK5

1vk5


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 598 4.797 %RANDOM
Rwork0.19 ---
obs0.192 12465 99.521 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 107.01 Å2 / Biso mean: 30.716 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.995 Å20.498 Å20 Å2
2--0.995 Å20 Å2
3----1.493 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 173 57 1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211109
X-RAY DIFFRACTIONr_angle_refined_deg2.3822.0741528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4122.39146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38115169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.229158
X-RAY DIFFRACTIONr_chiral_restr0.1640.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021859
X-RAY DIFFRACTIONr_mcbond_it1.3931.5575
X-RAY DIFFRACTIONr_mcangle_it2.4432942
X-RAY DIFFRACTIONr_scbond_it3.9223534
X-RAY DIFFRACTIONr_scangle_it5.3194.5586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0520.303380.24183491795.093
2.052-2.1080.217380.19684888899.775
2.108-2.1690.195370.17680684599.763
2.169-2.2360.236500.171801851100
2.236-2.3090.249370.16376180099.75
2.309-2.390.212340.181750784100
2.39-2.480.236370.18470974799.866
2.48-2.5810.266480.1970375299.867
2.581-2.6950.291340.207666700100
2.695-2.8260.268280.219658686100
2.826-2.9790.311300.202612642100
2.979-3.1590.254390.2573612100
3.159-3.3760.223180.19557575100
3.376-3.6450.204240.17518542100
3.645-3.9910.179270.156475502100
3.991-4.4580.209220.146438460100
4.458-5.1410.251220.172382404100
5.141-6.2810.328140.242339353100
6.281-8.8150.169100.231273283100
8.815-500.312110.2716418296.154

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