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- PDB-8awf: Xylose Isomerase in 80% relative humidity environment -

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Basic information

Entry
Database: PDB / ID: 8awf
TitleXylose Isomerase in 80% 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: 1.61 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
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9098
Polymers86,5672
Non-polymers3436
Water8,449469
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_455-x-1,-y,z1
Buried area33030 Å2
ΔGint-173 kcal/mol
Surface area46870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 98.750, 94.710
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
Components on special symmetry positions
IDModelComponents
11B-666-

HOH

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 47.72 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: 100 mM HEPES 200 mM Lithium Sulphate 34% Peg3350

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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: 1.61→43.78 Å / Num. obs: 1055859 / % possible obs: 99.04 % / Redundancy: 5.6 % / Biso Wilson estimate: 22.83 Å2 / CC1/2: 0.9909 / Net I/σ(I): 9.99
Reflection shellResolution: 1.61→1.668 Å / Num. unique obs: 10024 / CC1/2: 0.313

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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: 1.61→43.78 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 5440 5.17 %
Rwork0.1787 99706 -
obs0.1799 105146 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.11 Å2
Refinement stepCycle: LAST / Resolution: 1.61→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 16 469 6577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796338
X-RAY DIFFRACTIONf_angle_d0.97558591
X-RAY DIFFRACTIONf_chiral_restr0.0577879
X-RAY DIFFRACTIONf_plane_restr0.01141179
X-RAY DIFFRACTIONf_dihedral_angle_d5.5174887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.39681550.40043051X-RAY DIFFRACTION91.44
1.63-1.650.41641530.40233238X-RAY DIFFRACTION96.58
1.65-1.670.42011720.38183255X-RAY DIFFRACTION98.19
1.67-1.690.42511550.36873274X-RAY DIFFRACTION98.51
1.69-1.710.34041830.35083285X-RAY DIFFRACTION98.55
1.71-1.730.32811720.31873260X-RAY DIFFRACTION98.62
1.73-1.760.30841780.31253306X-RAY DIFFRACTION99.17
1.76-1.790.31691710.2963307X-RAY DIFFRACTION98.83
1.79-1.810.30521870.28093285X-RAY DIFFRACTION99.48
1.81-1.840.2991890.27133276X-RAY DIFFRACTION99.4
1.84-1.870.29811790.26063310X-RAY DIFFRACTION99.4
1.87-1.910.27051680.24753343X-RAY DIFFRACTION99.55
1.91-1.950.26311900.24873302X-RAY DIFFRACTION99.57
1.95-1.990.26041700.23883330X-RAY DIFFRACTION99.69
1.99-2.030.25961890.22113326X-RAY DIFFRACTION99.63
2.03-2.080.22111610.19213366X-RAY DIFFRACTION99.94
2.08-2.130.22551800.18313295X-RAY DIFFRACTION99.6
2.13-2.190.21061930.16713341X-RAY DIFFRACTION99.77
2.19-2.250.2241780.16043326X-RAY DIFFRACTION99.69
2.25-2.320.20411810.16123354X-RAY DIFFRACTION99.75
2.32-2.40.18621590.15213345X-RAY DIFFRACTION99.63
2.4-2.50.18231680.15483365X-RAY DIFFRACTION99.69
2.5-2.620.18061640.15653373X-RAY DIFFRACTION99.66
2.62-2.750.20071680.15083369X-RAY DIFFRACTION99.44
2.75-2.930.19591890.14853377X-RAY DIFFRACTION99.8
2.93-3.150.17432250.14783332X-RAY DIFFRACTION99.8
3.15-3.470.15522280.1393353X-RAY DIFFRACTION99.83
3.47-3.970.16652580.12983343X-RAY DIFFRACTION99.78
3.97-50.13451880.13053432X-RAY DIFFRACTION99.4
5-43.780.18131890.16983587X-RAY DIFFRACTION98.98

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