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- PDB-8awc: Xylose Isomerase in 85% relative humidity environment -

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Basic information

Entry
Database: PDB / ID: 8awc
TitleXylose Isomerase in 85% relative humidity environment
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose Isomerase / Glucose Isomerase / Humidity / Space group change / Unit cell change
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. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 29, 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

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4554
Polymers43,2831
Non-polymers1713
Water3,927218
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)173,81916
Polymers173,1334
Non-polymers68512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area32740 Å2
ΔGint-169 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.165, 94.506, 98.794
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-511-

HOH

21A-586-

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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.67 %
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: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→68.29 Å / Num. obs: 43526 / % possible obs: 75.57 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.4
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 2167 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RNF

6rnf


Resolution: 1.75→68.29 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 1442 4.6 %
Rwork0.1898 29890 -
obs0.1916 31332 75.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 1.75→68.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 8 218 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713221
X-RAY DIFFRACTIONf_angle_d0.91794373
X-RAY DIFFRACTIONf_chiral_restr0.0531445
X-RAY DIFFRACTIONf_plane_restr0.0098602
X-RAY DIFFRACTIONf_dihedral_angle_d5.0142457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.34032120.28323824X-RAY DIFFRACTION98.56
1.81-1.870.33511500.29272874X-RAY DIFFRACTION99.25
1.97-2.050.31481370.27192872X-RAY DIFFRACTION99.47
2.1-2.20.26861360.23443233X-RAY DIFFRACTION99.67
2.2-2.380.24651350.23142656X-RAY DIFFRACTION67.64
2.38-2.610.25031740.21783934X-RAY DIFFRACTION99.64
2.61-2.990.24261550.19153148X-RAY DIFFRACTION79.19
2.99-3.770.20141770.15953404X-RAY DIFFRACTION85.73
3.77-68.290.16151660.13083945X-RAY DIFFRACTION94.66

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