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- PDB-1gz5: Trehalose-6-phosphate synthase. OtsA -

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Basic information

Entry
Database: PDB / ID: 1gz5
TitleTrehalose-6-phosphate synthase. OtsA
ComponentsALPHA-TREHALOSE-PHOSPHATE SYNTHASE
KeywordsSYNTHASE / TREHALOSE / GLYCOSYLTRANSFERASE / ROSSMANN-FOLD / GLUCOSE-6-PHOSPHATE / TREHALOSE-6-PHOSPHATE
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to osmotic stress / response to stress / DNA damage response
Similarity search - Function
Alpha,alpha-trehalose-phosphate synthase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / IMIDAZOLE / URIDINE-5'-DIPHOSPHATE / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsGibson, R.P. / Turkenburg, J.P. / Davies, G.J.
Citation
Journal: Chem.Biol. / Year: 2002
Title: Insights Into Trehalose Synthesis Provided by the Structure of the Retaining Glycosyltransferase Otsa
Authors: Gibson, R.P. / Turkenburg, J.P. / Charnock, S.J. / Lloyd, R. / Davies, G.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Characterization of Escherichia Coli Otsa, a Trehalose-6-Phosphate Synthase from Glycosyltransferase Family 20
Authors: Gibson, R.P. / Lloyd, R.M. / Charnock, S.J. / Davies, G.J.
History
DepositionMay 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
B: ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
C: ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
D: ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,41916
Polymers207,4854
Non-polymers2,93412
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.612, 125.400, 176.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA1 - 2241 - 224
21SERSERPROPROBB1 - 2241 - 224
31SERSERPROPROCC1 - 2241 - 224
41SERSERPROPRODD1 - 2241 - 224
12ILEILEARGARGAA225 - 456225 - 456
22ILEILEARGARGBB225 - 456225 - 456
32ILEILEARGARGCC225 - 456225 - 456
42ILEILEARGARGDD225 - 456225 - 456

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.92739, -0.01896, 0.37361), (-0.02213, -0.99975, 0.0042), (0.37344, -0.01216, -0.92758)-10.22518, -10.11759, 51.50377
2given(-0.99999, 0.00438, -0.00175), (0.00403, 0.9856, 0.16904), (0.00246, 0.16903, -0.98561)-26.54259, -3.93221, 49.12816
3given(-0.9268, 0.01348, -0.3753), (0.0467, -0.98746, -0.15079), (-0.37264, -0.15728, 0.91455)-16.31909, -5.46956, -3.58459

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Components

#1: Protein
ALPHA-TREHALOSE-PHOSPHATE SYNTHASE / TREHALOSE-6-PHOSPHATE SYNTHASE / UDP-FORMING UDP-GLUCOSE-GLUCOSEPHOSPHATE / GLUCOSYLTRANSFERASE


Mass: 51871.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Description: C-TERMINAL HIS-TAG FUSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): B834
References: UniProt: P31677, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 53.3 %
Description: THESE STATISTICS REFLECT SEPARATE TREATMENT OF FREIDEL MATES DURING SCALING PROCEDURE. TRUE MULTIPLICITY IS THUS APPROXIMATALY TWICE THE VALUE GIVEN
Crystal growpH: 7.5
Details: 14% PEG4000, 0.15M NAAC, 0.1M IMIDAZOLE PH 7.5, 10MM MG-UDP, 10MM G6P
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
114 %(v/v)PEG400011
20.15 M11NaOAc
30.1 Mimidazole11pH7.5
4200 mM11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 86205 / % possible obs: 99.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.43

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.43→100 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.449 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.242
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: TLS REFINEMENT USED THROUGHOUT. MOLECULE C SHOWS LARGE DISORDER IN ITS N-TERMINAL DOMAIN REFLECTED IN LARGE TLS VALUES AND POOR ELECTRON DENSITY. RESIDUES ALA 208 B AND ALA 208 D COULD NOT ...Details: TLS REFINEMENT USED THROUGHOUT. MOLECULE C SHOWS LARGE DISORDER IN ITS N-TERMINAL DOMAIN REFLECTED IN LARGE TLS VALUES AND POOR ELECTRON DENSITY. RESIDUES ALA 208 B AND ALA 208 D COULD NOT BE BUILT INTO THE ELECTRON DENSITY DUE TO LARGE DISORDER FOUND IN THESE LOOP REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4320 5 %RANDOM
Rwork0.206 ---
obs0.207 81873 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2---2.53 Å20 Å2
3---3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.43→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14606 0 184 288 15078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02115164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.811.96420636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41551816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.22250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.27256
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4660.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5230.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.59092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.948214612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.03736072
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0874.56024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1799tight positional0.040.03
12B1799tight positional0.030.03
13C1799tight positional0.020.03
14D1799tight positional0.030.03
21A1850tight positional0.040.03
22B1850tight positional0.060.03
23C1850tight positional0.070.03
24D1850tight positional0.050.03
11A1799tight thermal0.220.5
12B1799tight thermal0.180.5
13C1799tight thermal0.140.5
14D1799tight thermal0.140.5
21A1850tight thermal0.250.5
22B1850tight thermal0.230.5
23C1850tight thermal0.260.5
24D1850tight thermal0.20.5
LS refinement shellResolution: 2.44→2.5 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 292
Rwork0.284 5728
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.14680.26950.28634.77610.87492.9628-0.06460.03310.23960.07310.1706-0.3638-0.21230.1908-0.1060.1252-0.05190.03290.0616-0.05370.107713.77915.971236.4291
22.27481.26140.03042.9754-0.03551.19810.1639-0.3650.07870.8142-0.1192-0.05990.03720.0312-0.04470.38180.01560.03970.1414-0.05440.02640.7756-3.079351.0575
34.7934-1.3377-1.28997.0445-0.08413.2195-0.31990.478-0.7933-0.34710.2071-0.73520.24250.00740.11280.1529-0.09240.19820.1662-0.20270.398415.798-26.3122.6556
42.11250.4808-0.31583.6971-1.16871.4656-0.57040.8612-0.2397-1.24790.4769-0.5020.2779-0.10830.09350.6397-0.37390.21990.5666-0.17420.12289.6404-6.78524.4194
57.20460.87121.47258.0398-0.23224.7768-0.57511.08152.329-0.55920.45651.6629-1.098-0.27290.11860.53380.0684-0.37370.57240.60391.8824-40.32318.097915.9463
62.77920.5273-0.42083.78560.05482.6825-0.84681.29580.9154-1.42111.10971.2096-0.0937-0.5275-0.26290.8899-0.6812-0.58431.10770.65670.6431-27.4121.6123-1.7386
76.3421.9697-0.41485.89970.97893.2921-0.22020.2003-0.06160.14880.02480.65520.3542-0.03360.19530.1026-0.03130.09750.3321-0.01550.4282-42.4861-26.194322.0517
83.92661.86950.6882.67631.44391.86630.172-0.48620.51620.5978-0.40070.97530.1839-0.36750.22860.3058-0.01430.31860.2756-0.09630.5699-36.2364-10.010743.3534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 224
2X-RAY DIFFRACTION2A225 - 456
3X-RAY DIFFRACTION3B1 - 224
4X-RAY DIFFRACTION4B225 - 456
5X-RAY DIFFRACTION5C1 - 224
6X-RAY DIFFRACTION6C225 - 456
7X-RAY DIFFRACTION7D1 - 224
8X-RAY DIFFRACTION8D225 - 456
Refinement
*PLUS
Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.95

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