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- PDB-2q4o: Ensemble refinement of the crystal structure of a lysine decarbox... -

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Basic information

Entry
Database: PDB / ID: 2q4o
TitleEnsemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At2g37210
ComponentsUncharacterized protein At2g37210/T2N18.3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / AT2G37210 / LYSINE DECARBOXYLASE-LIKE PROTEIN / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
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 / Re-refinement using ensemble model / Resolution: 1.95 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
#1: Journal: 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
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein At2g37210/T2N18.3
B: Uncharacterized protein At2g37210/T2N18.3
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-72 kcal/mol
Surface area14210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.403, 66.773, 98.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Number of models8

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Components

#1: Protein Uncharacterized protein At2g37210/T2N18.3


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, T2N18.3 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8L8B8
#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

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2A33.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2A33

2a33


Resolution: 1.95→46.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1678720.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2a33 and the first data set in the deposited structure factor file for 2a33 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2a33 and the first data set in the deposited structure factor file for 2a33 along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1336 5.1 %RANDOM
Rwork0.168 ---
obs0.168 26352 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.591 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.29 Å20 Å2
3---1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.95→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 11 222 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.95-2.070.2652195.10.20640510.0184333427098.5
2.07-2.230.2242255.20.15441110.0154340433699.9
2.23-2.460.21121550.14441280.0144347434399.9
2.46-2.810.2162295.20.15141630.01443944392100
2.81-3.540.2421950.17641950.01644144414100
3.54-46.960.21622950.17443680.01445974597100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param

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