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- PDB-4ovx: Crystal structure of Xylose isomerase domain protein from Plancto... -

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Basic information

Entry
Database: PDB / ID: 4ovx
TitleCrystal structure of Xylose isomerase domain protein from Planctomyces limnophilus DSM 3776
ComponentsXylose isomerase domain protein TIM barrel
KeywordsISOMERASE / Tim Barrel / Uncharacterised protein / MCSG / PSI-BIOLOGY / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Xylose isomerase domain protein TIM barrel
Similarity search - Component
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.253 Å
AuthorsChang, C. / Bigelow, L. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Crystal structure of Xylose isomerase domain protein from Planctomyces limnophilus DSM 3776
Authors: Chang, C. / Bigelow, L. / Endres, M. / Joachimiak, A.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords / struct_site
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _struct_site.details
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase domain protein TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2144
Polymers31,0281
Non-polymers1863
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.305, 88.305, 132.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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Components

#1: Protein Xylose isomerase domain protein TIM barrel


Mass: 31027.875 Da / Num. of mol.: 1 / Fragment: UNP residues 37-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_2642 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: D5SQK4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Lithium Chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 25577 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.098 / Χ2: 0.92 / Net I/av σ(I): 27 / Net I/σ(I): 7 / Num. measured all: 296247
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.2911.20.99612320.808100
2.29-2.3311.50.86712680.817100
2.33-2.3811.70.7512520.821100
2.38-2.4211.70.68112370.823100
2.42-2.4811.70.60112450.887100
2.48-2.5311.70.50112730.881100
2.53-2.611.80.44612700.895100
2.6-2.6711.80.3612490.956100
2.67-2.7511.90.312500.873100
2.75-2.8311.80.2512690.932100
2.83-2.9411.90.19812640.914100
2.94-3.0511.80.15112620.971100
3.05-3.1911.80.12712700.941100
3.19-3.3611.80.09612820.93100
3.36-3.5711.70.07212800.928100
3.57-3.8511.70.06212870.921100
3.85-4.2311.60.05912981.039100
4.23-4.8511.40.05913141.176100
4.85-6.1110.05413340.925100
6.1-5010.40.04214410.95399.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.3_1479)refinement
RefinementMethod to determine structure: SAD / Resolution: 2.253→37.855 Å / FOM work R set: 0.8362 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.244 1295 5.1 %
Rwork0.1982 24085 -
obs0.2005 25380 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.37 Å2 / Biso mean: 33.89 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 2.253→37.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 12 204 2324
Biso mean--40.17 41.72 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012189
X-RAY DIFFRACTIONf_angle_d1.1562935
X-RAY DIFFRACTIONf_chiral_restr0.047303
X-RAY DIFFRACTIONf_plane_restr0.005383
X-RAY DIFFRACTIONf_dihedral_angle_d13.835811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2534-2.34360.29011590.21862518267797
2.3436-2.45020.26991290.20012632276199
2.4502-2.57940.25191320.197226252757100
2.5794-2.7410.24771490.199926552804100
2.741-2.95250.25891530.204626492802100
2.9525-3.24950.2431550.198326642819100
3.2495-3.71930.27931540.201126922846100
3.7193-4.68460.21451300.184627472877100
4.6846-37.86080.21391340.201529033037100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9332-0.56490.69283.7473-0.49351.98420.0188-0.4730.22710.15810.10320.3097-0.0834-0.4552-0.13010.2242-0.0342-0.01150.365-0.03850.277512.417118.16219.0631
22.25480.20970.59661.39250.0551.11210.1079-0.62550.33550.2628-0.13980.2366-0.0508-0.37350.00770.2909-0.03640.03780.4535-0.07310.244320.622123.208831.2377
33.25060.64410.15831.6370.20391.68360.1964-0.3863-0.16630.3233-0.1279-0.12670.0896-0.1013-0.04620.2731-0.0284-0.05670.3078-0.00550.233135.833817.501629.8655
42.78030.07582.15911.45910.88863.21950.24450.1174-0.27680.09740.0076-0.20090.42590.13-0.23690.29890.0075-0.03750.2435-0.01520.252426.4717.814714.106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 149 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 221 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 313 )A0

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