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- PDB-5zyc: Crystal Structure of Glucose Isomerase Soaked with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5zyc
TitleCrystal Structure of Glucose Isomerase Soaked with Mn2+
ComponentsXylose isomerase
KeywordsISOMERASE / 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
ACETATE ION / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural analysis of substrate recognition by glucose isomerase in Mn2+binding mode at M2 site in S. rubiginosus
Authors: Bae, J.E. / Hwang, K.Y. / Nam, K.H.
History
DepositionMay 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: 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

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5145
Polymers43,2831
Non-polymers2314
Water6,143341
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)174,05720
Polymers173,1334
Non-polymers92416
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 area32990 Å2
ΔGint-143 kcal/mol
Surface area45680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.456, 97.921, 101.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xylose isomerase / Glucose Isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / Details: PEG 400, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→70.63 Å / Num. obs: 46646 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.059 / Rrim(I) all: 0.126 / Net I/σ(I): 20.69
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.364 / Num. unique obs: 2302 / CC1/2: 0.903 / Rpim(I) all: 0.059 / Rrim(I) all: 0.414 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4I

5y4i


Resolution: 1.75→70.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.713 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18411 2356 5.1 %RANDOM
Rwork0.1605 ---
obs0.16164 44284 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.262 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.75→70.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 10 342 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193177
X-RAY DIFFRACTIONr_bond_other_d0.0010.022898
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9534305
X-RAY DIFFRACTIONr_angle_other_deg0.88936672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13522.674172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66815506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0241539
X-RAY DIFFRACTIONr_chiral_restr0.1140.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
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_it1.4121.3231571
X-RAY DIFFRACTIONr_mcbond_other1.3411.321569
X-RAY DIFFRACTIONr_mcangle_it1.9011.9781973
X-RAY DIFFRACTIONr_mcangle_other1.9111.9781974
X-RAY DIFFRACTIONr_scbond_it2.3821.5981606
X-RAY DIFFRACTIONr_scbond_other2.3821.5981606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6682.3022333
X-RAY DIFFRACTIONr_long_range_B_refined4.72117.0333809
X-RAY DIFFRACTIONr_long_range_B_other4.7217.0343810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 157 -
Rwork0.202 3258 -
obs--99.68 %

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