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- PDB-8wdh: Crystal structure of glucose isomerase by fixed-target pink-beam ... -

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Basic information

Entry
Database: PDB / ID: 8wdh
TitleCrystal structure of glucose isomerase by fixed-target pink-beam serial synchrotron crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / xylose isomerase / serial crystallography / serial synchrotron 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
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
CitationJournal: Crystals / Year: 2023
Title: Fixed-Target Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II.
Authors: Nam, K.H.
History
DepositionSep 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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)43,0303
Polymers42,9811
Non-polymers492
Water5,134285
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)172,11812
Polymers171,9244
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Buried area28530 Å2
ΔGint-193 kcal/mol
Surface area51380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.138, 101.936, 105.156
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-765-

HOH

21A-776-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 42980.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 295 K / Method: microbatch / Details: Tris, ammonium sulfate, MgCl2

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.8366 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8366 Å / Relative weight: 1
ReflectionResolution: 1.7→71.94 Å / Num. obs: 55523 / % possible obs: 100 % / Redundancy: 161.7 % / CC1/2: 0.824 / Net I/σ(I): 4.67
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 5313 / CC1/2: 0.3688
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→7 Å / Cross valid method: FREE R-VALUE / σ(F): 27.76 / Phase error: 25.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2779 1992 3.66 %
Rwork0.251 --
obs0.2582 55523 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 285 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043116
X-RAY DIFFRACTIONf_angle_d0.8614218
X-RAY DIFFRACTIONf_dihedral_angle_d6.135430
X-RAY DIFFRACTIONf_chiral_restr0.048435
X-RAY DIFFRACTIONf_plane_restr0.009574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31811480.30223781X-RAY DIFFRACTION96
1.74-1.790.281390.30463793X-RAY DIFFRACTION96
1.79-1.840.30271480.30273745X-RAY DIFFRACTION96
1.84-1.90.33631350.31263833X-RAY DIFFRACTION97
1.9-1.960.28471390.28473775X-RAY DIFFRACTION96
1.96-2.040.33911380.27943790X-RAY DIFFRACTION96
2.04-2.130.29441450.29443820X-RAY DIFFRACTION96
2.13-2.240.31771450.29243824X-RAY DIFFRACTION96
2.24-2.380.25041370.25043803X-RAY DIFFRACTION97
2.38-2.550.29041400.26293835X-RAY DIFFRACTION96
2.55-2.790.30051450.24193824X-RAY DIFFRACTION96
2.79-3.160.26471450.23123855X-RAY DIFFRACTION96
3.16-3.870.24341430.20763881X-RAY DIFFRACTION96
3.87-70.23911450.21443972X-RAY DIFFRACTION96

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