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- PDB-8awy: Millisecond cryo-trapping by the spitrobot crystal plunger, Seria... -

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Basic information

Entry
Database: PDB / ID: 8awy
TitleMillisecond cryo-trapping by the spitrobot crystal plunger, Serial measurement Xylose Isomerase with 2,3-butanediol at 50ms
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose Isomerase / Glucose Isomerase / Humidity serial measurement / time-resolved crystallography
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Meso-2,3-Butanediol / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2023
Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.
Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4465
Polymers43,2831
Non-polymers1634
Water8,755486
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)173,78520
Polymers173,1334
Non-polymers65216
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 area31150 Å2
ΔGint-166 kcal/mol
Surface area46020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 102.350, 99.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

21A-681-

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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BU9 / Meso-2,3-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.79 %
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: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→71.27 Å / Num. obs: 62424 / % possible obs: 99.97 % / Redundancy: 662 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.9792 / Net I/σ(I): 9.7
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 6154 / CC1/2: 0.9519
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RNF

6rnf


Resolution: 1.6→71.27 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.7186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 3219 5.16 %
Rwork0.1743 59202 -
obs0.1753 62421 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→71.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 9 486 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053196
X-RAY DIFFRACTIONf_angle_d0.84654338
X-RAY DIFFRACTIONf_chiral_restr0.0481447
X-RAY DIFFRACTIONf_plane_restr0.009595
X-RAY DIFFRACTIONf_dihedral_angle_d5448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.26051300.23032527X-RAY DIFFRACTION100
1.62-1.650.20331270.20232553X-RAY DIFFRACTION99.96
1.65-1.680.20611440.18922551X-RAY DIFFRACTION100
1.68-1.710.17331220.18572578X-RAY DIFFRACTION100
1.71-1.740.1851480.1832539X-RAY DIFFRACTION99.93
1.74-1.770.1991330.17542560X-RAY DIFFRACTION100
1.77-1.810.19741580.17082542X-RAY DIFFRACTION100
1.81-1.840.2061280.17912548X-RAY DIFFRACTION100
1.85-1.890.21881470.18692556X-RAY DIFFRACTION100
1.89-1.940.22081650.19192536X-RAY DIFFRACTION100
1.94-1.990.21731900.21242465X-RAY DIFFRACTION99.92
1.99-2.050.19541700.18352534X-RAY DIFFRACTION99.96
2.05-2.110.19291390.17452572X-RAY DIFFRACTION99.96
2.11-2.190.19081440.16362571X-RAY DIFFRACTION100
2.19-2.270.17971350.1692557X-RAY DIFFRACTION99.89
2.28-2.380.17731560.16122570X-RAY DIFFRACTION100
2.38-2.50.16191350.16212584X-RAY DIFFRACTION100
2.5-2.660.19751120.17722616X-RAY DIFFRACTION99.96
2.66-2.870.18681440.17252549X-RAY DIFFRACTION100
2.87-3.150.17671410.1692624X-RAY DIFFRACTION100
3.15-3.610.18121130.15782622X-RAY DIFFRACTION100
3.61-4.550.18391150.15572676X-RAY DIFFRACTION100
4.55-71.270.2251230.18662772X-RAY DIFFRACTION99.86

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