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- PDB-8aw8: Xylose Isomerase in 70% relative humidity environment -

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Basic information

Entry
Database: PDB / ID: 8aw8
TitleXylose Isomerase in 70% 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: 1.63 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

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9098
Polymers86,5672
Non-polymers3436
Water7,891438
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: 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_565-x,-y+1,z1
Buried area33240 Å2
ΔGint-168 kcal/mol
Surface area46830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.826, 96.307, 97.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
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: 1.63→52.83 Å / Num. obs: 60298 / % possible obs: 61.88 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.9
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 1.6 / Num. unique obs: 3015 / CC1/2: 0.593

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Processing

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

6rnf


Resolution: 1.63→52.83 Å / SU ML: 0.1524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 3036 5.04 %
Rwork0.1598 57257 -
obs0.1615 60293 61.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.95 Å2
Refinement stepCycle: LAST / Resolution: 1.63→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 16 438 6546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086284
X-RAY DIFFRACTIONf_angle_d1.05438508
X-RAY DIFFRACTIONf_chiral_restr0.0535874
X-RAY DIFFRACTIONf_plane_restr0.01191160
X-RAY DIFFRACTIONf_dihedral_angle_d5.4122874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.3159220.2074564X-RAY DIFFRACTION13.37
1.66-1.690.2383470.2199847X-RAY DIFFRACTION20.46
1.69-1.710.252390.21631045X-RAY DIFFRACTION33.95
1.74-1.750.2564350.2356625X-RAY DIFFRACTION61.28
1.75-1.780.24451370.21182975X-RAY DIFFRACTION70.2
1.78-1.820.26751860.20923202X-RAY DIFFRACTION77.94
1.82-1.860.28461860.2093465X-RAY DIFFRACTION83.34
1.86-1.870.2697380.1987842X-RAY DIFFRACTION86.11
1.98-20.1996980.18151755X-RAY DIFFRACTION98.77
2-2.050.1991960.16093612X-RAY DIFFRACTION99.56
2.1-2.120.24791140.16491552X-RAY DIFFRACTION99.58
2.12-2.20.18762200.14784173X-RAY DIFFRACTION99.86
2.2-2.290.1697970.16591701X-RAY DIFFRACTION40.61
2.29-2.390.19092150.15394179X-RAY DIFFRACTION99.77
2.39-2.520.18232030.16074229X-RAY DIFFRACTION99.89
2.52-2.640.19931540.16123383X-RAY DIFFRACTION99.63
2.71-2.880.20431710.15783425X-RAY DIFFRACTION99.17
2.88-3.170.18432050.15724273X-RAY DIFFRACTION99.96
3.17-3.630.16682220.14713602X-RAY DIFFRACTION84.98
3.63-4.580.16511990.13483354X-RAY DIFFRACTION78.29
4.58-52.830.20082520.16324454X-RAY DIFFRACTION99.75

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