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- PDB-4w4q: Glucose isomerase structure determined by serial femtosecond crys... -

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Basic information

Entry
Database: PDB / ID: 4w4q
TitleGlucose isomerase structure determined by serial femtosecond crystallography at SACLA
ComponentsXylose isomerase
KeywordsISOMERASE / XFEL / glucose isomerase / xylose isomerase
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 / Resolution: 2 Å
AuthorsNango, E. / Tanaka, T. / Sugahara, M. / Suzuki, M. / Iwata, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT Japan
CitationJournal: Nat.Methods / Year: 2015
Title: Grease matrix as a versatile carrier of proteins for serial crystallography
Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / ...Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / Murata, M. / Inoue, T. / Tono, K. / Song, C. / Park, J. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Iwata, S.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_nat ...diffrn_source / entity_src_nat / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _entity_src_nat.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_beamline / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,3232
Polymers43,2831
Non-polymers401
Water6,107339
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)173,2948
Polymers173,1334
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area30850 Å2
ΔGint-154 kcal/mol
Surface area47790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 100.000, 103.000
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-507-

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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 278 K / Method: batch mode / pH: 8.5
Details: 40%(w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 33122 / % possible obs: 99.9 % / Redundancy: 85 % / Net I/σ(I): 3.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2→29.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.096 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 1675 5.1 %RANDOM
Rwork0.15905 ---
obs0.16094 31451 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 2→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 1 339 3386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193130
X-RAY DIFFRACTIONr_bond_other_d0.0010.022903
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9524239
X-RAY DIFFRACTIONr_angle_other_deg0.91236644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40122.941170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0981536
X-RAY DIFFRACTIONr_chiral_restr0.1120.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8862.161552
X-RAY DIFFRACTIONr_mcbond_other1.8812.1571551
X-RAY DIFFRACTIONr_mcangle_it2.5663.2251940
X-RAY DIFFRACTIONr_mcangle_other2.5653.2291941
X-RAY DIFFRACTIONr_scbond_it3.0512.5371578
X-RAY DIFFRACTIONr_scbond_other3.0452.5371578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7333.6722299
X-RAY DIFFRACTIONr_long_range_B_refined7.16319.0613792
X-RAY DIFFRACTIONr_long_range_B_other6.85318.3843657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 136 -
Rwork0.145 2274 -
obs--100 %

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