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- PDB-5avh: The 0.90 angstrom structure (I222) of glucose isomerase crystalli... -

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Basic information

Entry
Database: PDB / ID: 5avh
TitleThe 0.90 angstrom structure (I222) of glucose isomerase crystallized in high-strength agarose hydrogel
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase / hydrogel
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 / SYNCHROTRON / Resolution: 0.9 Å
AuthorsSugiyama, S. / Shimizu, N. / Maruyama, N. / Sazaki, G. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI23860028 Japan
JSPS KAKENHI2565005 Japan
JSPS KAKENHI25286051 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Growth of protein crystals in hydrogels prevents osmotic shock
Authors: Sugiyama, S. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
History
DepositionJun 16, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)43,0951
Polymers43,0951
Non-polymers00
Water9,278515
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19010 Å2
Unit cell
Length a, b, c (Å)93.268, 97.588, 102.490
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-562-

HOH

21A-787-

HOH

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Components

#1: Protein Xylose isomerase / glucose isomerase


Mass: 43095.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 0.1M Tris-HCl (pH 7.0), 10% (v/v) MPD, 0.1M Ca acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. obs: 325304 / % possible obs: 95.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.38 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 0.9→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.344 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12735 16000 5 %RANDOM
Rwork0.11628 ---
obs0.11683 300000 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 0.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 0 515 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193492
X-RAY DIFFRACTIONr_bond_other_d0.0020.023210
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9554762
X-RAY DIFFRACTIONr_angle_other_deg2.32837383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32623.112196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251542
X-RAY DIFFRACTIONr_chiral_restr0.1230.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214196
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02876
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_it0.8490.691721
X-RAY DIFFRACTIONr_mcbond_other0.8280.6881720
X-RAY DIFFRACTIONr_mcangle_it0.9761.0432188
X-RAY DIFFRACTIONr_mcangle_other1.0011.0442189
X-RAY DIFFRACTIONr_scbond_it1.9130.91771
X-RAY DIFFRACTIONr_scbond_other1.9050.8991771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1821.2932574
X-RAY DIFFRACTIONr_long_range_B_refined2.427.2844661
X-RAY DIFFRACTIONr_long_range_B_other1.9546.3954281
X-RAY DIFFRACTIONr_rigid_bond_restr11.5936702
X-RAY DIFFRACTIONr_sphericity_free17.7665155
X-RAY DIFFRACTIONr_sphericity_bonded5.58957094
LS refinement shellResolution: 0.9→0.923 Å
RfactorNum. reflection% reflection
Rfree0.237 1213 -
Rwork0.225 20000 -
obs--95.15 %

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