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- PDB-1vk5: X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680 -

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Basic information

Entry
Database: PDB / ID: 1vk5
TitleX-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680
Componentsexpressed protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / 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 / SYNCHROTRON / MAD / Resolution: 1.604 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Johnson, K.A. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: 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. / Bingman, C.A. / Johnson, K.A. / Wesenberg, G.E. / Bitto, E. / Jeon, W.B. / Phillips, G.N.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: expressed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1549
Polymers18,0031
Non-polymers1,1518
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: expressed protein
hetero molecules

A: expressed protein
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 area5890 Å2
ΔGint-90 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 83.450, 60.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein expressed protein


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


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


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / 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 / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.3863.63
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.5protein (10 mg/ml), Ammonium Sulfate (0.8M), Hepes (0.1M), Magnesium Sulfate (0.04M), CHAPS (0.41%), pH 8.5, Vapor diffusion, hanging drop, temperature 293K
2932vapor diffusion, hanging drop8.5protein (5 mg/ml), Ammonium Sulfate (0.8M), Hepes (0.1M), Magnesium Sulfate (0.04M), CHAPS (0.41%), pH 8.5, Vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.979
SYNCHROTRONAPS 32-ID20.96408, 0.97916, 0.97931
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDFeb 14, 2004Bent cylindrical Si-mirror (Rh coating)
MAR CCD 165 mm2CCDFeb 27, 2004Rh Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) double-crystalSINGLE WAVELENGTHMx-ray1
2Diamond 111 mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.964081
30.979161
40.979311
ReflectionResolution: 1.6→50 Å / Num. obs: 32231 / % possible obs: 99.2 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.61
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.6610.40.3029.31,292.2
1.66-1.720.2431,2100
1.72-1.80.1841,2100
1.8-1.90.1331,2100
1.9-2.020.0871,2100
2.02-2.170.0621,2100
2.17-2.390.0461,2100
2.39-2.740.0361,2100
2.74-3.450.0271,2100
3.45-500.0211,299.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 1.693 Å / D res low: 20 Å / FOM : 0.72 / Reflection: 26563
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97932.8-9.69
1120.97927.1-7.44
1130.96413.44-3.46
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
126.09723.2870.47SE16.20.77
243.28111.5348.799SE17.30.78
3-5.40137.7221.013SE23.60.8
436.7943.8999.425SE20.40.66
515.49356.2831.613SE32.50.56
Phasing MAD shell
Resolution (Å)FOM Reflection
6-200.891311
3.82-60.92223
2.99-3.820.92865
2.54-2.990.873345
2.25-2.540.833787
2.04-2.250.74168
1.88-2.040.564390
1.75-1.880.414474
Phasing dmFOM : 0.79 / FOM acentric: 0.8 / FOM centric: 0.77 / Reflection: 26623 / Reflection acentric: 24711 / Reflection centric: 1912
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.8-19.7850.980.980.941197979218
3-4.80.970.980.9136233239384
2.4-30.940.950.8745664212354
2.1-2.40.890.90.8245784276302
1.8-2.10.720.730.6380237576447
1.7-1.80.50.50.3946364429207

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.05phasing
RESOLVE2.05phasing
ARP/wARPmodel building
REFMACrefmac_5.1.24refinement
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.604→34.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.982 / SU ML: 0.035 / SU R Cruickshank DPI: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 1633 5.071 %RANDOM
Rwork0.1599 ---
all0.161 ---
obs0.16102 30570 99.99 %-
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 mean: 23.618 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.604→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 63 172 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221128
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9921532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6895120
X-RAY DIFFRACTIONr_chiral_restr0.1180.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02800
X-RAY DIFFRACTIONr_nbd_refined0.220.2530
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.221
X-RAY DIFFRACTIONr_mcbond_it1.4952616
X-RAY DIFFRACTIONr_mcangle_it2.82141014
X-RAY DIFFRACTIONr_scbond_it3.6266512
X-RAY DIFFRACTIONr_scangle_it5.3598518
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 (%)
1.604-1.6460.2571160.2192223234099.96
1.646-1.6910.2351290.20521772306
1.691-1.73990.1911290.19320942223
1.74-1.79330.2061120.17920382150
1.793-1.85190.1991130.17219952108
1.852-1.91670.1931060.16419242030
1.917-1.98880.192980.15718811979
1.989-2.06970.1681080.15217801888
2.07-2.16140.169920.15417321824
2.161-2.26650.187880.14916471735
2.266-2.38850.174790.14815951674
2.388-2.53260.176730.1515071580
2.533-2.70640.165600.14314131473
2.706-2.92170.181660.15613091375
2.922-3.19830.186720.16212291301
3.198-3.57190.175510.14911161167
3.572-4.1170.155520.1429771029
4.117-5.02430.155500.137836886
5.024-7.03040.321290.206681710
7.03-34.29970.125100.201416428

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