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- PDB-1ydh: X-ray structure of a lysine decarboxylase-like protein from arabi... -

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Basic information

Entry
Database: PDB / ID: 1ydh
TitleX-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950
ComponentsAt5g11950
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG / AT5G11950 / LYSINE DECARBOXYLASE-LIKE PROTEIN
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / protein homodimerization activity / nucleus / plasma membrane / 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
NITRATE ION / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.152 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / 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
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 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 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: At5g11950
B: At5g11950
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7897
Polymers48,4782
Non-polymers3105
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-21 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.589, 80.427, 50.709
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

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Components

#1: Protein At5g11950


Mass: 24239.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT5G11950 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q84MC2
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.63 %
Description: UNMODELED DENSITY BETWEEN ASP 94A AND ILE 133B IS POSSIBLY DUE TO AN L-LYSINE MOLECULE
Crystal growTemperature: 293 K / pH: 7
Details: 10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794
DetectorType: APS-1 / Detector: CCD / Date: Dec 15, 2004
Details: SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR: WATER COOLED
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.152→35.451 Å / Num. obs: 25771 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.384 / Χ2: 0.951 / Net I/σ(I): 6.266
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.15-2.236.20.3842.40124600.657100
2.28-2.370.3324740.65100
2.37-2.480.3124650.691100
2.48-2.610.25824820.802100
2.61-2.770.22924680.939100
2.77-2.990.19724811.092100
2.99-3.290.16624731.157100
3.29-3.760.14224891.209100
3.76-4.740.12725001.163100
4.74-500.11925371.10599.6

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.3 Å / D res low: 30 Å / FOM : 0.27 / Reflection: 19977
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
120.0860.0545.01SE27.80.62
290.25521.26812.549SE24.80.59
315.681.68420.177SE34.10.71
461.3839.95713.454SE53.30.67
524.6083.55919.156SE36.80.65
683.77626.25319.511SE230.5
792.10828.05816.003SE32.80.53
864.3636.18912.147SE32.20.62
915.6358.52316.537SE43.30.66
1081.09429.7844.881SE19.20.45
1199.19633.7163.067SE55.40.88
1292.51136.15414.191SE32.50.48
1375.8833.89718.398SE28.20.48
14102.07330.4872.86SE46.50.66
1590.22517.14824.296SE30.30.38
1689.74212.52122.627SE50.70.55
Phasing MAD shell
Resolution (Å)FOM Reflection
8.19-300.391020
5.2-8.190.361738
4.07-5.20.322232
3.46-4.070.312614
3.06-3.460.32866
2.77-3.060.253003
2.55-2.770.23205
2.37-2.550.163299
Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.67 / Reflection: 19977 / Reflection acentric: 19237 / Reflection centric: 740
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-29.6940.920.920.84939835104
4.1-6.60.90.90.7528292671158
3.3-4.10.850.860.7735633412151
2.9-3.30.720.720.6434383329109
2.5-2.90.530.530.5557835639144
2.3-2.50.340.340.293425335174

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2.152→35.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.159 / SU B: 4.455 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.0000, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1300 5.063 %RANDOM
Rwork0.159 ---
all0.16164 ---
obs0.16164 25679 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.915 Å20 Å20.386 Å2
2---0.158 Å20 Å2
3----0.584 Å2
Refinement stepCycle: LAST / Resolution: 2.152→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 20 319 3137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.983839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73323.729118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83615516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8451519
X-RAY DIFFRACTIONr_chiral_restr0.1120.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022111
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21968
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.57921872
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65642860
X-RAY DIFFRACTIONr_scbond_it5.12161136
X-RAY DIFFRACTIONr_scangle_it6.9858979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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 (%)
2.152-2.2080.304730.1881698191192.674
2.208-2.2680.2231050.1841740185299.622
2.268-2.3340.255750.1761717179799.722
2.334-2.4050.254980.1821667177099.718
2.405-2.4840.26890.1821576166899.82
2.484-2.5710.292800.1721575165999.759
2.571-2.6680.268810.1761516160799.378
2.668-2.7770.199840.1741434152399.672
2.777-2.90.218680.1731386146899.046
2.9-3.0410.219750.1591323140399.644
3.041-3.2060.211670.1611271134799.332
3.206-3.40.199710.151186126599.368
3.4-3.6340.212600.1441142120699.668
3.634-3.9240.199540.1371042110199.546
3.924-4.2970.167610.1369641025100
4.297-4.8010.175400.13885925100
4.801-5.5390.188370.144782819100
5.539-6.7730.19340.18675709100
6.773-9.5290.214300.165512542100
9.529-66.5190.179180.17728832095.625

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