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

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Basic information

Entry
Database: PDB / ID: 6irk
TitleCrystal structure of glucose isomerase by fixed-target serial femtosecond crystallography
ComponentsXylose isomerase
KeywordsISOMERASE / xylose isomerase / SFX
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. / 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, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (Korea)2017M3A9F6029736 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.
Authors: Lee, D. / Baek, S. / Park, J. / Lee, K. / Kim, J. / Lee, S.J. / Chung, W.K. / Lee, J.L. / Cho, Y. / Nam, K.H.
History
DepositionNov 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split
Revision 1.3Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_R_split
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_related_exp_data_set / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.5Nov 22, 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
Water3,765209
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 area31050 Å2
ΔGint-188 kcal/mol
Surface area46100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.050, 99.000, 101.920
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-510-

HOH

21A-691-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Fragment: UNP residues 3-388 / 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.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.89 %
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: 296 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: CSI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 29, 2018 / Frequency: 30 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.75→71.94 Å / Num. obs: 47861 / % possible obs: 100 % / Redundancy: 356.8 % / CC1/2: 0.9284 / R split: 0.2163 / Net I/σ(I): 4.03
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 125.2 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 4736 / CC1/2: 0.796 / R split: 0.6471 / % possible all: 100
Serial crystallography measurementCollection time total: 1.2 hours / Collimation: Kirkpatrick-Baez mirrors / Focal spot size: 4 µm2 / Pulse duration: 20 fsec. / Pulse photon energy: 9700 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: 10000 / Sample dehydration prevention: seal / Sample holding: mesh / Sample unit size: 60 µm
Serial crystallography data reductionFrame hits: 79805 / Frames indexed: 29157 / Frames total: 134325 / Lattices indexed: 29157 / XFEL pulse events: 10000 / XFEL run numbers: 14

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4J

5y4j


Resolution: 1.75→71.013 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.99
RfactorNum. reflection% reflection
Rfree0.203 1988 4.17 %
Rwork0.1818 --
obs0.1827 47666 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→71.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 2 209 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013122
X-RAY DIFFRACTIONf_angle_d1.0784227
X-RAY DIFFRACTIONf_dihedral_angle_d9.7622561
X-RAY DIFFRACTIONf_chiral_restr0.054435
X-RAY DIFFRACTIONf_plane_restr0.008576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.63141370.65613239X-RAY DIFFRACTION100
1.7938-1.84230.36251410.35943252X-RAY DIFFRACTION100
1.8423-1.89650.24461390.22193191X-RAY DIFFRACTION100
1.8965-1.95770.21741470.17433193X-RAY DIFFRACTION100
1.9577-2.02770.21871400.19173273X-RAY DIFFRACTION100
2.0277-2.10890.21531480.16693199X-RAY DIFFRACTION100
2.1089-2.20490.19221360.14983229X-RAY DIFFRACTION100
2.2049-2.32110.18151380.15883245X-RAY DIFFRACTION100
2.3211-2.46660.20051440.15473257X-RAY DIFFRACTION100
2.4666-2.6570.20641390.1733285X-RAY DIFFRACTION100
2.657-2.92440.19941450.17963264X-RAY DIFFRACTION100
2.9244-3.34760.18811430.1773276X-RAY DIFFRACTION100
3.3476-4.21750.18971390.17693326X-RAY DIFFRACTION100
4.2175-71.07190.20071520.18913449X-RAY DIFFRACTION100

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