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- PDB-7dmm: Structure of a glucose isomerase crystal grown in an aqueous glyc... -

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Basic information

Entry
Database: PDB / ID: 7dmm
TitleStructure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants
ComponentsXylose isomerase
KeywordsISOMERASE / ISOMERASE(INTRAMOLEC
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. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsSuzuki, Y. / Maita, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K04960 Japan
CitationJournal: To be published
Title: Extraordinarily fast growth of high-quality glucose isomerase crystals simply by concentration in a precipitant-free solution with a cryoprotectant
Authors: Suzuki, Y. / Ikemitsu, N. / Maita, N.
History
DepositionDec 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)43,4006
Polymers43,0661
Non-polymers3345
Water5,459303
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)173,60124
Polymers172,2644
Non-polymers1,33720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area34390 Å2
ΔGint-222 kcal/mol
Surface area44900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.610, 98.460, 102.300
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-752-

HOH

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Components

#1: Protein Xylose isomerase / Glucose isomerase


Mass: 43065.988 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: batch mode
Details: precipitant-free in 30(v/v)% aqueous glycerol solution

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.99→70.94 Å / Num. obs: 256074 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.9
Reflection shellResolution: 0.99→1.01 Å / Rmerge(I) obs: 0.308 / Num. unique obs: 12629 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIB

1xib


Resolution: 0.99→51.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.246 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16564 13077 5.1 %RANDOM
Rwork0.15693 ---
obs0.15736 242981 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 0.99→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 15 303 3357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193242
X-RAY DIFFRACTIONr_bond_other_d0.0020.022948
X-RAY DIFFRACTIONr_angle_refined_deg2.291.9554408
X-RAY DIFFRACTIONr_angle_other_deg1.12436822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05623.24179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76115523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981536
X-RAY DIFFRACTIONr_chiral_restr0.130.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213754
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02738
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_it0.9530.8261582
X-RAY DIFFRACTIONr_mcbond_other0.9210.8251581
X-RAY DIFFRACTIONr_mcangle_it1.2841.251985
X-RAY DIFFRACTIONr_mcangle_other1.2921.2511986
X-RAY DIFFRACTIONr_scbond_it2.3071.0471660
X-RAY DIFFRACTIONr_scbond_other2.3031.0471660
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1931.5072409
X-RAY DIFFRACTIONr_long_range_B_refined3.62610.5873755
X-RAY DIFFRACTIONr_long_range_B_other3.53210.343699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.991→1.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 882 -
Rwork0.233 17907 -
obs--99.31 %

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