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- PDB-3u95: Crystal structure of a putative alpha-glucosidase from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 3u95
TitleCrystal structure of a putative alpha-glucosidase from Thermotoga neapolitana
ComponentsGlycoside hydrolase, family 4
KeywordsHYDROLASE / Hydrolysis / Cytosol
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
LDH C-terminal domain-like / AglA-like glucosidase / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Glycoside hydrolase, family 4
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsHa, N.C. / Jun, S.Y. / Yun, B.Y. / Yoon, B.Y. / Piao, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure and thermostability of a putative alpha-glucosidase from Thermotoga neapolitana
Authors: Yun, B.Y. / Jun, S.Y. / Kim, N.A. / Yoon, B.Y. / Piao, S. / Park, S.H. / Jeong, S.H. / Lee, H. / Ha, N.C.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase, family 4
B: Glycoside hydrolase, family 4
C: Glycoside hydrolase, family 4
D: Glycoside hydrolase, family 4
E: Glycoside hydrolase, family 4
F: Glycoside hydrolase, family 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,50212
Polymers338,1726
Non-polymers3306
Water44,6952481
1
A: Glycoside hydrolase, family 4
B: Glycoside hydrolase, family 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8344
Polymers112,7242
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-25 kcal/mol
Surface area36650 Å2
MethodPISA
2
C: Glycoside hydrolase, family 4
D: Glycoside hydrolase, family 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8344
Polymers112,7242
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-26 kcal/mol
Surface area36410 Å2
MethodPISA
3
E: Glycoside hydrolase, family 4
F: Glycoside hydrolase, family 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8344
Polymers112,7242
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-22 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.532, 154.532, 139.065
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Glycoside hydrolase, family 4


Mass: 56362.027 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: CTN_1830 / Production host: Escherichia coli (E. coli) / References: UniProt: B9KAM3
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2481 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M ethanolamine, 2% 1,4-dioxane, 8% PEG 20000, 1mM DTT, 1mM MnCl2, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: Double Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. all: 248951 / Num. obs: 246434 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 25.98
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.66 / Num. unique all: 24470 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→40.904 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1985 80 %RANDOM
Rwork0.1851 ---
obs0.1854 246434 98.85 %-
all-248951 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.664 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7556 Å20 Å2-0 Å2
2---0.7556 Å2-0 Å2
3---1.5112 Å2
Refinement stepCycle: LAST / Resolution: 1.998→40.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23329 0 6 2481 25816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723927
X-RAY DIFFRACTIONf_angle_d1.0332390
X-RAY DIFFRACTIONf_dihedral_angle_d15.2569082
X-RAY DIFFRACTIONf_chiral_restr0.0753404
X-RAY DIFFRACTIONf_plane_restr0.0054183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.998-2.04790.28351460.26517040X-RAY DIFFRACTION96
2.0479-2.10330.28651430.23817507X-RAY DIFFRACTION98
2.1033-2.16520.24321390.220617525X-RAY DIFFRACTION98
2.1652-2.23510.281350.205217644X-RAY DIFFRACTION98
2.2351-2.31490.25721400.202117574X-RAY DIFFRACTION99
2.3149-2.40760.25891430.197717614X-RAY DIFFRACTION99
2.4076-2.51720.24491430.195717587X-RAY DIFFRACTION99
2.5172-2.64990.23321440.195817779X-RAY DIFFRACTION99
2.6499-2.81580.24841450.193517737X-RAY DIFFRACTION99
2.8158-3.03320.23471470.193317713X-RAY DIFFRACTION99
3.0332-3.33830.2531400.182917753X-RAY DIFFRACTION100
3.3383-3.82110.19311370.163717830X-RAY DIFFRACTION100
3.8211-4.81290.15561460.146217796X-RAY DIFFRACTION100
4.8129-40.91270.19861370.177717745X-RAY DIFFRACTION99

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