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- PDB-1q4r: Gene Product of At3g17210 from Arabidopsis Thaliana -

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Basic information

Entry
Database: PDB / ID: 1q4r
TitleGene Product of At3g17210 from Arabidopsis Thaliana
Componentsprotein At3g17210
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / Arabidopsis Thaliana / Center for Eukaryotic Structural Genomics / Protein Structure Initiative / CESG
Function / homology
Function and homology information


defense response to fungus / defense response to bacterium / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stress-response A/B barrel domain-containing protein HS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPhillips Jr., G.N. / Bingman, C.A. / Johnson, K.A. / Smith, D.W. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana
Authors: Bingman, C.A. / Johnson, K.A. / Peterson, F.C. / Frederick, R.O. / Zhao, Q. / Thao, S. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Smith, D.W. / Newman, C.S. / Ulrich, E.L. / Hegeman, A. / ...Authors: Bingman, C.A. / Johnson, K.A. / Peterson, F.C. / Frederick, R.O. / Zhao, Q. / Thao, S. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Smith, D.W. / Newman, C.S. / Ulrich, E.L. / Hegeman, A. / Sussman, M.R. / Markley, J.L. / Phillips Jr., G.N.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: 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 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein At3g17210
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6002
Polymers12,5761
Non-polymers241
Water1,964109
1
A: protein At3g17210
hetero molecules

A: protein At3g17210
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2014
Polymers25,1522
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3380 Å2
ΔGint-42 kcal/mol
Surface area10440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.468, 55.468, 57.673
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Cell settinghexagonal
Space group name H-MP62
DetailsThe second part of the biological assembly is generated by the two fold axis:-x, -y, z and a translation of 0 1 0

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Components

#1: Protein protein At3g17210


Mass: 12576.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g17210 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9LUV2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.95 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium MES, Sodium citrate, MEthyl Ether PEG 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %(w/v)mPEG50001reservoir
2120 mMsodium cirtate1reservoir
3100 mMsodium HEPES1reservoirpH6.0
4100 mM1dropNaCl
510 mMsodium HEPES1droppH7.0
614 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 7570 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 35.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.06 / Num. unique all: 598 / % possible all: 75.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 14162 / % possible obs: 93.5 % / Redundancy: 5.2 % / Num. measured all: 75176
Reflection shell
*PLUS
% possible obs: 52.6 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SOLVERESOLVEphasing
REFMAC5.1.24refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.331 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 369 4.9 %RANDOM
Rwork0.18217 ---
all0.18469 7209 --
obs0.18469 7209 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 1 109 928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021850
X-RAY DIFFRACTIONr_bond_other_d0.0020.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9491153
X-RAY DIFFRACTIONr_angle_other_deg1.02531806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855102
X-RAY DIFFRACTIONr_chiral_restr0.3380.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02918
X-RAY DIFFRACTIONr_gen_planes_other0.010.02161
X-RAY DIFFRACTIONr_nbd_refined0.2160.2164
X-RAY DIFFRACTIONr_nbd_other0.2440.2837
X-RAY DIFFRACTIONr_nbtor_other0.0910.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.215
X-RAY DIFFRACTIONr_mcbond_it1.0581.5519
X-RAY DIFFRACTIONr_mcangle_it1.8512844
X-RAY DIFFRACTIONr_scbond_it2.7963331
X-RAY DIFFRACTIONr_scangle_it4.4824.5309
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 27 -
Rwork0.258 342 -
obs-598 75.2 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.861

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