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- PDB-6ll2: Crystal structure of glucose isomerase by fixed-target serial fem... -

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Basic information

Entry
Database: PDB / ID: 6ll2
TitleCrystal structure of glucose isomerase by fixed-target serial femtosecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / serial crystallography / sfx
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. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of glucose isomerase by fixed-target serial femtosecond crystallography
Authors: Nam, K.H.
History
DepositionDec 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water6,972387
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 area31240 Å2
ΔGint-189 kcal/mol
Surface area44820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.630, 98.230, 101.607
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-514-

HOH

21A-741-

HOH

31A-794-

HOH

41A-825-

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.: 387 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
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: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 10, 2019 / Details: Kirkpatrick-Baez mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.75→70.9 Å / Num. obs: 47004 / % possible obs: 100 % / Redundancy: 346.2 % / CC1/2: 0.934777 / CC star: 0.9397 / Net I/σ(I): 5.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 124.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4650 / CC1/2: 0.7908 / CC star: 0.9397 / % possible all: 100
Serial crystallography measurementXFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: polyimide sealing / Sample holding: viscous medium / Support base: x-y translation stage
Serial crystallography data reductionFrame hits: 33438 / Frames indexed: 22412 / Frames total: 55307

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYE

5zye


Resolution: 1.75→70.623 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.51
RfactorNum. reflection% reflection
Rfree0.1965 1341 2.85 %
Rwork0.1717 --
obs0.1724 46993 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.8 Å2 / Biso mean: 13.1837 Å2 / Biso min: 1.17 Å2
Refinement stepCycle: final / Resolution: 1.75→70.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 387 3411
Biso mean--5.93 27.29 -
Num. residues----384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.75-1.81260.25761360.21934516
1.8126-1.88510.20321270.19714504
1.8851-1.97090.24411340.1724517
1.9709-2.07490.20451350.1494498
2.0749-2.20490.1781310.14274547
2.2049-2.37510.16991330.14714546
2.3751-2.61410.17691360.15664552
2.6141-2.99240.17521320.16434595
2.9924-3.77010.19841370.17754604
3.7701-70.6230.21491400.2064773

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