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- PDB-6qnj: Liquid Application Method for time-resolved Analyses (LAMA) by se... -

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Basic information

Entry
Database: PDB / ID: 6qnj
TitleLiquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 4.5 s timepoint
ComponentsXylose isomerase
KeywordsISOMERASE / Complex / Diffusion / Dynamics
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / alpha-D-glucopyranose / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.851 Å
AuthorsMehrabi, P. / Schulz, E.C. / Miller, R.J.D.
CitationJournal: Nat.Methods / Year: 2019
Title: Liquid application method for time-resolved analyses by serial synchrotron crystallography.
Authors: Mehrabi, P. / Schulz, E.C. / Agthe, M. / Horrell, S. / Bourenkov, G. / von Stetten, D. / Leimkohl, J.P. / Schikora, H. / Schneider, T.R. / Pearson, A.R. / Tellkamp, F. / Miller, R.J.D.
History
DepositionFeb 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Derived calculations / Refinement description / Category: pdbx_struct_conn_angle / refine / struct_conn / Item: _refine.pdbx_diffrn_id
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5474
Polymers43,2831
Non-polymers2633
Water4,900272
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-20 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.620, 99.380, 87.630
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-514-

HOH

21A-690-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH pH 7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9778 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.851→49.69 Å / Num. obs: 35418 / % possible obs: 99.66 % / Redundancy: 119.4 % / Net I/σ(I): 5.2
Reflection shellResolution: 1.851→1.92 Å
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.851→49.69 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1733 4.9 %
Rwork0.1802 --
obs0.1816 35386 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.851→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 14 272 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063149
X-RAY DIFFRACTIONf_angle_d0.8024266
X-RAY DIFFRACTIONf_dihedral_angle_d2.172578
X-RAY DIFFRACTIONf_chiral_restr0.222442
X-RAY DIFFRACTIONf_plane_restr0.006580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8511-1.90560.4211490.33892658X-RAY DIFFRACTION97
1.9056-1.96710.32831440.28722765X-RAY DIFFRACTION100
1.9671-2.03740.25621400.23992794X-RAY DIFFRACTION100
2.0374-2.1190.25061670.20912745X-RAY DIFFRACTION100
2.119-2.21540.25591550.19522781X-RAY DIFFRACTION100
2.2154-2.33220.23111310.18492784X-RAY DIFFRACTION100
2.3322-2.47830.23661360.17742819X-RAY DIFFRACTION100
2.4783-2.66960.2181150.18072827X-RAY DIFFRACTION100
2.6696-2.93830.18241260.16672839X-RAY DIFFRACTION100
2.9383-3.36340.18151320.15572851X-RAY DIFFRACTION100
3.3634-4.23710.14261150.13352888X-RAY DIFFRACTION100
4.2371-49.70790.16082230.15962902X-RAY DIFFRACTION100

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