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- PDB-2q45: Ensemble refinement of the protein crystal structure of putative ... -

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Basic information

Entry
Database: PDB / ID: 2q45
TitleEnsemble refinement of the protein crystal structure of putative tropinone reductase from Arabidopsis thaliana gene At1g07440
ComponentsPutative tropinone reductase homolog At1g07440
KeywordsOXIDOREDUCTASE / Ensemble Refinement / Refinement Methodology Development / AT1G07440 / REDUCTIVELY METHYLATED PROTEIN / PUTATIVE TROPINONE REDUCTASE / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / extracellular region
Similarity search - Function
Tropinone reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tropinone reductase homolog At1g07440 / Tropinone reductase homolog At1g07450
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.1 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: 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.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tropinone reductase homolog At1g07440


Theoretical massNumber of molelcules
Total (without water)28,3601
Polymers28,3601
Non-polymers00
Water1,02757
1
A: Putative tropinone reductase homolog At1g07440

A: Putative tropinone reductase homolog At1g07440

A: Putative tropinone reductase homolog At1g07440

A: Putative tropinone reductase homolog At1g07440


Theoretical massNumber of molelcules
Total (without water)113,4414
Polymers113,4414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11710 Å2
ΔGint-71 kcal/mol
Surface area34200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.335, 76.599, 112.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Number of models8
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

22A-305-

HOH

33A-305-

HOH

44A-305-

HOH

55A-305-

HOH

66A-305-

HOH

77A-305-

HOH

88A-305-

HOH

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Components

#1: Protein Putative tropinone reductase homolog At1g07440


Mass: 28360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At1g07440, F22G5_16, F22G5.20, F22G5.39 / Plasmid: pVP-13 (pQE derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) p(LacI+RARE)
References: UniProt: Q9ASX2, UniProt: P0DKI3*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.13 Å3/Da / Density % sol: 42.31 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XQ1.

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Data collection

DetectorType: APS-1
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 1XQ1

1xq1


Resolution: 2.1→38.3 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 117821.039 / 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 1xq1 and the first data set in the deposited structure factor file for 1xq1 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1xq1 and the first data set in the deposited structure factor file for 1xq1 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
Rfree0.295 729 5 %RANDOM
Rwork0.234 ---
obs0.234 14467 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.04 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.59 Å20 Å20 Å2
2---1.56 Å20 Å2
3----4.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 57 1689
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.712.5
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 (%)
2.1-2.230.2921325.60.21622330.0252374236599.6
2.23-2.40.31514260.22722350.0262379237799.9
2.4-2.650.2581355.60.21722730.02224092408100
2.65-3.030.2721104.60.2222790.0262391238999.9
3.03-3.810.286953.90.22323450.0292443244099.9
3.81-38.30.3191154.60.25523730.032547248897.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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