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

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Basic information

Entry
Database: PDB / ID: 5brp
TitleCrystal structure of Bacillus licheniformis trehalose-6-phosphate hydrolase (TreA), mutant R201Q, in complex with PNG
ComponentsGlycoside Hydrolase Family 13
KeywordsHYDROLASE / trehalose-6-phosphate / PNG / GH13 family / TIM barrel
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
4-nitrophenyl alpha-D-glucopyranoside / Glycoside Hydrolase Family 13
Similarity search - Component
Biological speciesBacillus licheniformis ATCC 14580 = DSM 13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 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)267,45411
Polymers266,4534
Non-polymers1,0017
Water29,9591663
1
A: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9393
Polymers66,6131
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21930 Å2
MethodPISA
2
B: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9393
Polymers66,6131
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area22010 Å2
MethodPISA
3
C: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9393
Polymers66,6131
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area21850 Å2
MethodPISA
4
D: Glycoside Hydrolase Family 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6382
Polymers66,6131
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.252, 97.388, 108.539
Angle α, β, γ (deg.)80.30, 88.15, 72.18
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 66613.242 Da / Num. of mol.: 4 / Mutation: R201Q
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: Sugar ChemComp-PNG / 4-nitrophenyl alpha-D-glucopyranoside / 4'-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE / 4-nitrophenyl alpha-D-glucoside / 4-nitrophenyl D-glucoside / 4-nitrophenyl glucoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
4'-nitrophenyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1663 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 3350, 0.1 M magnesium acetate hexahydrate, 2% Tacsimate (pH 4.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.985 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 141603 / % possible obs: 97.5 % / Redundancy: 3.7 % / Net I/σ(I): 32

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
AUTOMAR1.8.1_1168phasing
Coot0.7.1model building
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BRQ

5brq


Resolution: 2.05→30 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 1997 1.41 %
Rwork0.1708 --
obs0.1714 141228 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18344 0 67 1663 20074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818914
X-RAY DIFFRACTIONf_angle_d1.09125613
X-RAY DIFFRACTIONf_dihedral_angle_d14.5616982
X-RAY DIFFRACTIONf_chiral_restr0.082595
X-RAY DIFFRACTIONf_plane_restr0.0053338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0468-2.09790.30291220.24968674X-RAY DIFFRACTION42
2.0979-2.15460.25981400.207310058X-RAY DIFFRACTION48
2.1546-2.21790.22971470.19559951X-RAY DIFFRACTION49
2.2179-2.28940.28151420.22389788X-RAY DIFFRACTION48
2.2894-2.37110.26551460.187310048X-RAY DIFFRACTION49
2.3711-2.46590.24151320.179310002X-RAY DIFFRACTION49
2.4659-2.57780.24831470.182110035X-RAY DIFFRACTION49
2.5778-2.71340.26321430.187810077X-RAY DIFFRACTION49
2.7134-2.88290.24381430.183910066X-RAY DIFFRACTION49
2.8829-3.10470.22421490.185610070X-RAY DIFFRACTION49
3.1047-3.41560.21721440.173410100X-RAY DIFFRACTION49
3.4156-3.90650.18231510.152210113X-RAY DIFFRACTION49
3.9065-4.90880.17711410.134510156X-RAY DIFFRACTION49
4.9088-19.54710.16351500.147510093X-RAY DIFFRACTION49

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