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- PDB-2a33: X-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabi... -

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Basic information

Entry
Database: PDB / ID: 2a33
TitleX-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabidopsis Thaliana Gene AT2G37210
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG / AT2G37210 / LYSINE DECARBOXYLASE-LIKE PROTEIN
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / hydrolase activity, hydrolyzing N-glycosyl compounds / nucleus / cytosol
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Mccoy, J.G. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2006
Title: X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210.
Authors: Jeon, W.B. / Allard, S.T.M. / Bingman, C.A. / Bitto, E. / Han, B.W. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 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: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0495
Polymers47,8332
Non-polymers2163
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-74 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.403, 66.773, 98.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein


Mass: 23916.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g37210 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: GenBank: 21805708, UniProt: Q8L8B8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 296 K / pH: 6.5
Details: 10 MG/ML PROTEIN, 22% PEG 2K, 0.084 M MAGNESIUM SULFATE, 0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 296K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97625
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: WATER COOLED SI (111) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionRedundancy: 10.7 % / Number: 26424 / Rmerge(I) obs: 0.1 / Χ2: 0.881 / D res high: 1.95 Å / D res low: 50 Å / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25010010.0451.3813.9
3.334.210010.0731.26614.6
2.913.3310010.1230.80214.7
2.652.9110010.2090.71214.3
2.462.6510010.2720.68312.4
2.312.4610010.2990.6789.8
2.22.3110010.2990.6848.3
2.12.210010.3490.6667.4
2.022.199.910.4150.6616.2
1.952.0298.610.5180.6164.8
ReflectionResolution: 1.95→50 Å / Num. obs: 26424 / % possible obs: 99.8 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.009
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.756 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.459 / Cor.coef. Fo:Fc: 0.498
Highest resolutionLowest resolution
Rotation3 Å46.96 Å
Translation3 Å46.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.6data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDH

1ydh


Resolution: 1.95→46.984 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.676 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1336 5.1 %RANDOM
Rwork0.181 ---
obs0.183 25025 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 11 222 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222686
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9793618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46624.444108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.021514
X-RAY DIFFRACTIONr_chiral_restr0.1350.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021972
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21829
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.86121781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.94642729
X-RAY DIFFRACTIONr_scbond_it5.34261034
X-RAY DIFFRACTIONr_scangle_it7.1468889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 96 -
Rwork0.215 1777 -
obs--97.45 %

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