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- PDB-5brq: Crystal structure of Bacillus licheniformis trehalose-6-phosphate... -

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Basic information

Entry
Database: PDB / ID: 5brq
TitleCrystal structure of Bacillus licheniformis trehalose-6-phosphate hydrolase (TreA)
ComponentsGlycoside Hydrolase Family 13
KeywordsHYDROLASE / trehalose-6-phosphate hydrolase / TIM barrel / GH13 family
Function / homology
Function and homology information


alpha,alpha-phosphotrehalase activity / trehalose catabolic process / metal ion binding / cytoplasm
Similarity search - Function
Trehalose-6-phosphate hydrolase / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Trehalose-6-phosphate hydrolase / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycoside Hydrolase Family 13
Similarity search - Component
Biological speciesBacillus licheniformis ATCC 14580 = DSM 13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsHsiao, C.-D. / Lin, M.-G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Bacillus licheniformis trehalose-6-phosphate hydrolase structures suggest keys to substrate specificity
Authors: Lin, M.-G. / Chi, M.-C. / Naveen, V. / Li, Y.-C. / Lin, L.-L. / Hsiao, C.-D.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 13
B: Glycoside Hydrolase Family 13
C: Glycoside Hydrolase Family 13
D: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,6668
Polymers266,5694
Non-polymers974
Water26,0321445
1
A: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,6421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21820 Å2
MethodPISA
2
B: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,6421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21830 Å2
MethodPISA
3
C: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,6421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21830 Å2
MethodPISA
4
D: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6672
Polymers66,6421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.802, 97.584, 108.336
Angle α, β, γ (deg.)98.20, 91.44, 108.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glycoside Hydrolase Family 13 / / trehalose-6-phosphate hydrolase


Mass: 66642.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis ATCC 14580 = DSM 13 (bacteria)
Strain: ATCC 14580 = DSM 13 / Gene: treA, BL03069 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15 / References: UniProt: Q65MI2, EC: 3.2.1.93
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1445 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% (w/v) PEG 3350, 0.2 M magnesium acetate hexahydrate, 2% Tacsimate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.903 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 149079 / % possible obs: 96.8 % / Redundancy: 3.8 % / Net I/σ(I): 29

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Processing

SoftwareName: PHENIX / Version: 1.8.1_1168 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOK

1uok


Resolution: 2.003→24.304 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 2002 1.37 %
Rwork0.1808 --
obs0.1817 146093 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.003→24.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18352 0 4 1445 19801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818856
X-RAY DIFFRACTIONf_angle_d1.11425528
X-RAY DIFFRACTIONf_dihedral_angle_d14.2736984
X-RAY DIFFRACTIONf_chiral_restr0.0812580
X-RAY DIFFRACTIONf_plane_restr0.0053332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0027-2.05270.31321110.23568135X-RAY DIFFRACTION37
2.0527-2.10820.31111350.22619562X-RAY DIFFRACTION44
2.1082-2.17020.28321490.217410244X-RAY DIFFRACTION47
2.1702-2.24020.28361520.210810400X-RAY DIFFRACTION48
2.2402-2.32020.28821420.210610552X-RAY DIFFRACTION48
2.3202-2.4130.25561380.204810522X-RAY DIFFRACTION48
2.413-2.52270.25851510.199610557X-RAY DIFFRACTION49
2.5227-2.65560.26271380.203410591X-RAY DIFFRACTION49
2.6556-2.82170.28561470.209510569X-RAY DIFFRACTION49
2.8217-3.03920.26061480.204610621X-RAY DIFFRACTION49
3.0392-3.34440.25021510.189910605X-RAY DIFFRACTION49
3.3444-3.82670.22991480.161510545X-RAY DIFFRACTION49
3.8267-4.81510.22261400.138610364X-RAY DIFFRACTION48
4.8151-24.30550.17921520.144810824X-RAY DIFFRACTION50

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