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- PDB-7vt9: CRYSTAL STRUCTURE AT 3.4 ANGSTROMS RESOLUTION OF Maltodextrin glu... -

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Basic information

Entry
Database: PDB / ID: 7vt9
TitleCRYSTAL STRUCTURE AT 3.4 ANGSTROMS RESOLUTION OF Maltodextrin glucosidase, MalZ, FROM Escherichia coli
ComponentsMaltodextrin glucosidase
KeywordsHYDROLASE / Alpha-amylase / Maltodextrin glucosidase
Function / homology
Function and homology information


alpha-glucan catabolic process / maltose metabolic process / alpha-1,4-glucosidase activity / alpha-glucosidase / protein homodimerization activity / cytoplasm
Similarity search - Function
Maltodextrin glucosidase / Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set ...Maltodextrin glucosidase / Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Maltodextrin glucosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAhn, W.-C. / Ahn, Y. / Woo, E.-J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8025599 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A2C2011328 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Dimeric architecture of maltodextrin glucosidase (MalZ) provides insights into the substrate recognition and hydrolysis mechanism.
Authors: Ahn, W.C. / An, Y. / Song, K.M. / Park, K.H. / Lee, S.J. / Oh, B.H. / Park, J.T. / Woo, E.J.
History
DepositionOct 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin glucosidase
B: Maltodextrin glucosidase


Theoretical massNumber of molelcules
Total (without water)140,8122
Polymers140,8122
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-11 kcal/mol
Surface area43560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.186, 204.186, 267.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 604 / Label seq-ID: 1 - 604

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.0246912371563, -0.999667243429, 0.00746627230298), (-0.999665315024, -0.0247474881892, -0.0075378887199), (0.00772015192353, -0.00727765365577, -0.999943715922)Vector: ...NCS oper: (Code: given
Matrix: (0.0246912371563, -0.999667243429, 0.00746627230298), (-0.999665315024, -0.0247474881892, -0.0075378887199), (0.00772015192353, -0.00727765365577, -0.999943715922)
Vector: -0.0760326104703, -1.29667442099, -137.93932711)

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Components

#1: Protein Maltodextrin glucosidase / Alpha-glucosidase


Mass: 70406.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: malZ, b0403, JW0393 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P21517, alpha-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.05 Å3/Da / Density % sol: 75.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% polyacrylic acid 5100, 100 mM HEPES/Sodium hydroxide pH 7.0 and 20 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→40.91 Å / Num. obs: 43678 / % possible obs: 99.9 % / Redundancy: 25.4 % / Biso Wilson estimate: 80.22 Å2 / Rmerge(I) obs: 0.355 / Net I/σ(I): 4.02
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.001 / Num. unique obs: 4169 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0G

2d0g


Resolution: 3.3→40.91 Å / SU ML: 0.6527 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.0566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3431 1960 4.67 %
Rwork0.3032 40042 -
obs0.3051 42002 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.69 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9762 0 0 1 9763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014610060
X-RAY DIFFRACTIONf_angle_d1.82913696
X-RAY DIFFRACTIONf_chiral_restr0.09391396
X-RAY DIFFRACTIONf_plane_restr0.01261812
X-RAY DIFFRACTIONf_dihedral_angle_d6.01031330
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.25651080492 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.40921160.40742289X-RAY DIFFRACTION80.43
3.38-3.470.42671270.38832713X-RAY DIFFRACTION93.88
3.47-3.570.3841530.38242846X-RAY DIFFRACTION99.14
3.57-3.690.34161370.35352870X-RAY DIFFRACTION100
3.69-3.820.37591440.33382880X-RAY DIFFRACTION100
3.82-3.970.37491410.32952901X-RAY DIFFRACTION99.97
3.97-4.150.40471410.33512898X-RAY DIFFRACTION99.87
4.15-4.370.36931450.32112900X-RAY DIFFRACTION99.9
4.37-4.650.33791410.30652900X-RAY DIFFRACTION100
4.65-50.36681410.28422906X-RAY DIFFRACTION99.97
5-5.510.34471380.282924X-RAY DIFFRACTION100
5.51-6.30.30461520.29032946X-RAY DIFFRACTION99.9
6.3-7.930.32571430.28612977X-RAY DIFFRACTION99.94
7.93-40.910.27721410.23013092X-RAY DIFFRACTION99.11
Refinement TLS params.Method: refined / Origin x: 23.5358538903 Å / Origin y: -23.6310403161 Å / Origin z: -68.7830396425 Å
111213212223313233
T0.739278735866 Å20.100995342622 Å20.188582855456 Å2-0.726078211949 Å20.142331859133 Å2--0.679651825925 Å2
L1.21307787762 °20.322369887935 °2-0.248049392124 °2-0.991546951759 °2-0.161987951793 °2--0.401486968497 °2
S0.0233359703939 Å °-0.204836892955 Å °-0.122451734808 Å °-0.307577819494 Å °0.115195770612 Å °-0.148526162744 Å °-0.0518559151446 Å °-0.150229324784 Å °-0.154353961756 Å °
Refinement TLS groupSelection details: all

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