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- PDB-1vjh: Crystal structure of gene product of At1g24000 from Arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 1vjh
TitleCrystal structure of gene product of At1g24000 from Arabidopsis thaliana
ComponentsBet v I allergen family
KeywordsPLANT PROTEIN / Structural genomics / Arabidopsis Thaliana / Center for Eukaryotic Structural Genomics / Protein Structure Initiative / CESG
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytosol
Similarity search - Function
: / Pathogenesis-related protein Bet v I family / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein At1g24000 / MLP-like protein 423
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Johnson, K.A. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: 1H, 15N and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana.
Authors: Song, J. / Zhao, Q. / Lee, M.S. / Markley, J.L.
History
DepositionFeb 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS ARE UNCERTAIN OF THE BIOLOGICAL UNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bet v I allergen family
B: Bet v I allergen family


Theoretical massNumber of molelcules
Total (without water)27,7472
Polymers27,7472
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.681, 34.261, 78.597
Angle α, β, γ (deg.)90.000, 90.008, 90.000
Int Tables number3
Cell settingmonoclinic
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-166-

HOH

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Components

#1: Protein Bet v I allergen family


Mass: 13873.567 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g24000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LR93, UniProt: P0C0B0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 7.5
Details: Sodium Malonate, Sodium HEPES, DMEPEG 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, hanging drop
Crystal grow
*PLUS
Method: unknown
Details: Aceti, D.J., (2003) Biopolymers, 469., Jeon, W.B., (2005) J.Struct.Funct.Genom., 61, 206., Zhao, Q., (2004) J.Struct.Funct.Genom., 5, 87.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97921 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 14582 / % possible obs: 99.8 % / Rmerge(I) obs: 0.065
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obs
2.1-2.141000.1
2.14-2.181000.099
2.18-2.221000.097
2.22-2.261000.099
2.26-2.311000.095
2.31-2.371000.096
2.37-2.421000.083
2.42-2.491000.087
2.49-2.561000.084
2.56-2.651000.081
2.65-2.741000.078
2.74-2.851000.077
2.85-2.981000.075
2.98-3.141000.07
3.14-3.331000.063
3.33-3.591000.058
3.59-3.951000.055
3.95-4.5299.60.052
4.52-5.6999.40.056
5.69-3097.50.067

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.1 Å / D res low: 30 Å / FOM : 0.45 / Reflection: 14224
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
19.248011.819SE15.82.38
244.49817.48124.397SE28.11.9
33.51925.81821.587SE162.14
49.3948.3196.505SE26.51.94
Phasing MAD shell
Resolution (Å)FOM Reflection
7.51-300.45700
4.76-7.510.471185
3.72-4.760.481531
3.16-3.720.491808
2.79-3.160.491975
2.53-2.790.472189
2.33-2.530.452373
2.17-2.330.362463
Phasing dmFOM : 0.66 / FOM acentric: 0.67 / FOM centric: 0.56 / Reflection: 14229 / Reflection acentric: 13044 / Reflection centric: 1185
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-29.7930.870.870.62648508140
3.8-60.870.880.7719351703232
3-3.80.80.810.6324392216223
2.6-30.680.70.5324102235175
2.3-2.60.580.590.4542283961267
2.1-2.30.440.450.3325692421148

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.1.24refinement
SOLVE2.02phasing
RESOLVE2.02phasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.4data extraction
RefinementResolution: 2.1→21.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.033 / SU ML: 0.114 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 733 5.031 %RANDOM
Rwork0.1857 ---
all0.188 ---
obs-13837 99.4 %-
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: 24.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.414 Å20 Å20.322 Å2
2--1.182 Å20 Å2
3----0.768 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 106 2015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221951
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9462624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775238
X-RAY DIFFRACTIONr_chiral_restr0.1120.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021418
X-RAY DIFFRACTIONr_nbd_refined0.2040.2788
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.218
X-RAY DIFFRACTIONr_mcbond_it1.1331.51193
X-RAY DIFFRACTIONr_mcangle_it2.03321943
X-RAY DIFFRACTIONr_scbond_it3.2973758
X-RAY DIFFRACTIONr_scangle_it5.2964.5681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.15060.231510.1429991092
2.151-2.20950.238570.1539701027
2.21-2.27350.248510.1629971048
2.274-2.34340.222480.168894942
2.343-2.42020.277520.179930982
2.42-2.50510.242450.165864909
2.505-2.59960.272480.173854902
2.6-2.70560.25330.177821854
2.706-2.82570.326430.185793836
2.826-2.96350.218400.197729769
2.963-3.12350.303250.199761786
3.313-3.5410.229330.188650683
3.541-3.8240.191390.182597636
3.824-4.1880.202330.178549583
4.188-4.68070.161280.187492524
4.681-5.40170.284220.191449474
5.402-6.6080.279230.263386410
6.608-9.31260.323260.244284318
9.313-79.05690.184140.225147190
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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