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- PDB-7cvm: Crystal structure of glucose isomerase by fixed-target serial syn... -

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Basic information

Entry
Database: PDB / ID: 7cvm
TitleCrystal structure of glucose isomerase by fixed-target serial synchrotron crystallography (500 ms)
ComponentsXylose isomerase
KeywordsISOMERASE / room temperature structure / serial crystallography / serial synchrotron crystallography
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
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Crystals / Year: 2020
Title: Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder
Authors: Park, S.Y. / Choi, H. / Eo, C. / Cho, Y. / Nam, K.H.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.3Nov 29, 2023Group: Refinement description / Category: 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)43,3323
Polymers43,2831
Non-polymers492
Water5,747319
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)173,32812
Polymers173,1334
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area31300 Å2
ΔGint-200 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.550, 100.260, 103.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 293.5 K / Method: batch mode / pH: 7 / Details: Tris-HCl, Ammonium sulfate, Magnesium sulfate

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→72.46 Å / Num. obs: 33589 / % possible obs: 100 % / Redundancy: 30.8 % / CC1/2: 0.7069 / CC star: 0.9101 / Net I/σ(I): 2.05
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 3282 / CC1/2: 0.5605 / CC star: 0.8475
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: Polyimide films / Sample holding: Nylon mesh

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4I

5y4i


Resolution: 2→72.05 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1993 5.93 %
Rwork0.2136 31590 -
obs0.2156 33583 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.41 Å2 / Biso mean: 19.2822 Å2 / Biso min: 4.61 Å2
Refinement stepCycle: final / Resolution: 2→72.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 2 319 3354
Biso mean--12.89 28.27 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.28791460.238722122358
2.05-2.110.26381430.234922122355
2.11-2.170.2421360.222322192355
2.17-2.240.29531400.221322302370
2.24-2.320.26081370.229722332370
2.32-2.410.25921400.223722562396
2.41-2.520.29411410.229422382379
2.52-2.650.28021470.232122402387
2.65-2.820.30991360.226522462382
2.82-3.040.26741400.210722612401
3.04-3.340.22081470.199122682415
3.34-3.830.20191420.190422722414
3.83-4.820.20331460.191223072453
4.82-72.050.24611520.2223962548

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