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- PDB-5zfs: Crystal structure of Arthrobacter globiformis M30 sugar epimerase... -

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Basic information

Entry
Database: PDB / ID: 5zfs
TitleCrystal structure of Arthrobacter globiformis M30 sugar epimerase which can produce D-allulose from D-fructose
ComponentsD-allulose-3-epimerase
KeywordsISOMERASE / Epimerase
Function / homology
Function and homology information


Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding / carbohydrate metabolic process
Similarity search - Function
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 / : / Ketose 3-epimerase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYoshida, H. / Yoshihara, A. / Gullapalli, P.K. / Ohtani, K. / Akimitsu, K. / Izumori, K. / Kamitori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07271 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose.
Authors: Yoshida, H. / Yoshihara, A. / Gullapalli, P.K. / Ohtani, K. / Akimitsu, K. / Izumori, K. / Kamitori, S.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-allulose-3-epimerase
B: D-allulose-3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4309
Polymers65,0252
Non-polymers4057
Water6,792377
1
A: D-allulose-3-epimerase
B: D-allulose-3-epimerase
hetero molecules

A: D-allulose-3-epimerase
B: D-allulose-3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,86018
Polymers130,0504
Non-polymers81014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area14450 Å2
ΔGint-57 kcal/mol
Surface area36810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.980, 103.980, 256.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein D-allulose-3-epimerase


Mass: 32512.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: DAE / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A1L7NQ96
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: AMMONIUM ACETATE, SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→45.02 Å / Num. obs: 59179 / % possible obs: 99 % / Redundancy: 22.556 % / Biso Wilson estimate: 28.637 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.08 / Χ2: 1.026 / Net I/σ(I): 31.46 / Num. measured all: 1334865 / Scaling rejects: 551
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.96-2.014.6520.334.5939460.9080.36991.5
2.01-2.079.7420.2887.6140900.9730.30496.8
2.07-2.1313.5160.23711.1540500.9850.24698.5
2.13-2.1917.7780.20515.1139790.9920.21299.8
2.19-2.2622.520.18817.9738910.9950.192100
2.26-2.3426.890.16522.2937410.9970.168100
2.34-2.4328.1180.1524.9736470.9970.15399.9
2.43-2.5328.7090.13827.7735080.9980.1499.9
2.53-2.6428.1990.11931.7233670.9980.12199.9
2.64-2.7726.5810.10634.6932280.9980.10899.9
2.77-2.9227.1620.09638.5930660.9980.098100
2.92-3.129.1950.08345.2729320.9990.084100
3.1-3.3128.490.07549.7627570.9990.07699.9
3.31-3.5827.4090.06854.1125880.9990.069100
3.58-3.9224.6470.06256.2824000.9990.063100
3.92-4.3824.3220.05858.8421780.9990.06100
4.38-5.0626.7140.05463.1419530.9990.055100
5.06-6.226.290.05560.0116800.9990.056100
6.2-8.7723.6960.04758.75135210.049100
8.77-45.0224.3310.03962.418260.9980.0498.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYL

3vyl


Resolution: 1.96→45.02 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.859 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2980 5 %RANDOM
Rwork0.1856 ---
obs0.1869 56104 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.83 Å2 / Biso mean: 23.161 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.96→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 22 379 4887
Biso mean--30.23 31.72 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194598
X-RAY DIFFRACTIONr_bond_other_d00.024306
X-RAY DIFFRACTIONr_angle_refined_deg0.7181.956230
X-RAY DIFFRACTIONr_angle_other_deg0.52539879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44723.879214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9731530
X-RAY DIFFRACTIONr_chiral_restr0.0550.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025298
X-RAY DIFFRACTIONr_gen_planes_other00.021070
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 213 -
Rwork0.204 3729 -
all-3942 -
obs--91.59 %

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