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- PDB-3m16: Structure of a Transaldolase from Oleispira antarctica -

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Basic information

Entry
Database: PDB / ID: 3m16
TitleStructure of a Transaldolase from Oleispira antarctica
ComponentsTransaldolase
KeywordsTRANSFERASE / Oleispira antarctica / transaldolase / dimer / molecular replacement / Swiss-Model / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytosol
Similarity search - Function
Transaldolase type 1 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsSinger, A.U. / Kagan, O. / Zhang, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat Commun / Year: 2013
Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Sep 6, 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 / struct_conn / struct_ref_seq
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.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transaldolase


Theoretical massNumber of molelcules
Total (without water)36,2881
Polymers36,2881
Non-polymers00
Water23413
1
A: Transaldolase

A: Transaldolase


Theoretical massNumber of molelcules
Total (without water)72,5762
Polymers72,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1780 Å2
ΔGint-13 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.105, 143.105, 119.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein Transaldolase


Mass: 36288.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: OLEI02190 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: U3KRE8*PLUS, EC: 2.2.1.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.88 Å3/Da / Density % sol: 74.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4M sodium formate, 3mM magnesium chloride, cryoprotected in Paratone-N oil (Hampton), VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97942, 0.97972
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2009 / Details: Mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979721
ReflectionResolution: 2.8→35.78 Å / Num. all: 18484 / Num. obs: 18469 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 26.2 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 57.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.734 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ONR

1onr


Resolution: 2.79→35.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.472 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24886 947 5.1 %RANDOM
Rwork0.20914 ---
obs0.21114 17475 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.79→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 0 13 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9643436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72625.514107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3411511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021862
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.21297
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21780
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 64 -
Rwork0.353 1255 -
obs--98.88 %

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