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

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Basic information

Entry
Database: PDB / ID: 6rnd
TitleLiquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 15 ms 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionMay 8, 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 1.2Jul 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 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)43,5124
Polymers43,2831
Non-polymers2293
Water4,378243
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,04816
Polymers173,1334
Non-polymers91512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area33300 Å2
ΔGint-175 kcal/mol
Surface area46490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 99.400, 87.600
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-686-

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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 48.29 %
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: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.699→68.526 Å / Num. obs: 45700 / % possible obs: 99.99 % / Redundancy: 492.9 % / Net I/σ(I): 5.36
Reflection shellResolution: 1.699→1.737 Å / Num. unique obs: 4499

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBN

3kbn


Resolution: 1.7→68.526 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.2112 2239 4.9 %
Rwork0.1644 --
obs0.1665 45697 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→68.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 14 243 3303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123149
X-RAY DIFFRACTIONf_angle_d1.2424266
X-RAY DIFFRACTIONf_dihedral_angle_d2.3262578
X-RAY DIFFRACTIONf_chiral_restr0.226442
X-RAY DIFFRACTIONf_plane_restr0.009580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7370.31751620.26972658X-RAY DIFFRACTION100
1.737-1.77740.31541630.25662650X-RAY DIFFRACTION100
1.7774-1.82180.29561380.24352676X-RAY DIFFRACTION100
1.8218-1.87110.3191480.24632674X-RAY DIFFRACTION100
1.8711-1.92620.29671460.25422700X-RAY DIFFRACTION100
1.9262-1.98830.27461640.21382669X-RAY DIFFRACTION100
1.9883-2.05940.27231100.20542720X-RAY DIFFRACTION100
2.0594-2.14190.24771640.19292691X-RAY DIFFRACTION100
2.1419-2.23940.23311520.17182654X-RAY DIFFRACTION100
2.2394-2.35740.18321500.16932693X-RAY DIFFRACTION100
2.3574-2.50510.19521440.1632716X-RAY DIFFRACTION100
2.5051-2.69860.18791440.1612729X-RAY DIFFRACTION100
2.6986-2.97010.17111280.14832718X-RAY DIFFRACTION100
2.9701-3.39990.18221030.1452798X-RAY DIFFRACTION100
3.3999-4.28340.17221190.12342797X-RAY DIFFRACTION100
4.2834-68.58210.16831040.13512915X-RAY DIFFRACTION100

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