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- PDB-1xq1: X-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS ... -

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Basic information

Entry
Database: PDB / ID: 1xq1
TitleX-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS THALIANA GENE AT1G07440
ComponentsPUTATIVE TROPINONE REDUCATSE
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / CESG / AT1G07440 / REDUCTIVELY METHYLATED PROTEIN / PUTATIVE TROPINONE REDUCTASE / PSI / Center for Eukaryotic Structural Genomics
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS THALIANA GENE AT1G07440
Authors: Center for Eukaryotic Structural Genomics
History
DepositionOct 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 REDUCATSE


Theoretical massNumber of molelcules
Total (without water)28,3601
Polymers28,3601
Non-polymers00
Water1,02757
1
A: PUTATIVE TROPINONE REDUCATSE

A: PUTATIVE TROPINONE REDUCATSE


Theoretical massNumber of molelcules
Total (without water)56,7212
Polymers56,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2030 Å2
ΔGint-13 kcal/mol
Surface area20910 Å2
MethodPISA
2
A: PUTATIVE TROPINONE REDUCATSE

A: PUTATIVE TROPINONE REDUCATSE

A: PUTATIVE TROPINONE REDUCATSE

A: PUTATIVE TROPINONE REDUCATSE


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 area11960 Å2
ΔGint-72 kcal/mol
Surface area33920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.335, 76.599, 112.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

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Components

#1: Protein PUTATIVE TROPINONE REDUCATSE


Mass: 28360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07440 / 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
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 MG/ML PROTEIN, 12 PERCENT MEPEG 2000, 0.21 M AMMONIUM SULFATE, 0.10 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: APS-1 / Detector: CCD / Date: Jul 31, 2004
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→38.3 Å / Num. all: 14486 / Num. obs: 14488 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 25.4 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 36 / Limit k min: 0 / Limit l max: 53 / Limit l min: 0 / Observed criterion F max: 117786.47 / Observed criterion F min: 0.3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.533
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.1-2.1560.3275.659310.92299.9
2.15-2.20.2729550.998100
2.2-2.260.2469620.979100
2.26-2.330.2079491.016100
2.33-2.40.1739491.122100
2.4-2.490.1399511.103100
2.49-2.590.1149601.154100
2.59-2.710.0999811.211100
2.71-2.850.0789681.027100
2.85-3.030.0629481.079100
3.03-3.260.0519800.97599.9
3.26-3.590.0459741.147100
3.59-4.110.0419881.19399.9
4.11-5.180.0349931.02699.9
5.18-500.0229990.98594.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å38.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AE1

1ae1


Resolution: 2.1→38.3 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.316 729 5 %random
Rwork0.255 ---
all-14583 --
obs-14486 99.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.0751 Å2 / ksol: 0.360732 e/Å3
Displacement parametersBiso max: 77 Å2 / Biso mean: 36.62 Å2 / Biso min: 18.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.62 Å20 Å20 Å2
2---1.34 Å20 Å2
3----4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 57 1689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_torsion_deg21.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.69
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.190.2938750.24116540.0311782174197.7
2.19-2.310.32810760.26816900.0321798179799.9
2.31-2.450.3191156.40.25716920.031809180799.9
2.45-2.640.29995.50.25317060.0291810180599.7
2.64-2.910.335874.80.25717090.03617961796100
2.91-3.330.308703.80.24717660.0371837183699.9
3.33-4.190.238844.60.23717370.0261822182199.9
4.19-38.30.409804.20.27318030.0461942188396.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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