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- PDB-5hxa: Crystal structure of an UDP-forming alpha, alpha-terhalose-phosph... -

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Basic information

Entry
Database: PDB / ID: 5hxa
TitleCrystal structure of an UDP-forming alpha, alpha-terhalose-phosphate synthase from Burkholderia xenovorans
ComponentsAlpha,alpha-trehalose-phosphate synthase (UDP-forming)
KeywordsPROTEIN BINDING / SSGCID / Burkholderia / UDP / UDP-forming / alpha / alpha-trehalose-phosphate synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process
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
Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an UDP-forming alpha, alpha-terhalose-phosphate synthase from Burkholderia xenovorans
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_conn_angle / 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_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,15014
Polymers54,3911
Non-polymers75913
Water7,746430
1
A: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules

A: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,29928
Polymers108,7822
Non-polymers1,51826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area6690 Å2
ΔGint6 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.180, 171.180, 95.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-891-

HOH

21A-959-

HOH

31A-1023-

HOH

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Components

#1: Protein Alpha,alpha-trehalose-phosphate synthase (UDP-forming) / Osmoregulatory trehalose synthesis protein A / Trehalose-6-phosphate synthase


Mass: 54390.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_A3374 / Plasmid: BrovA.00010.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q142X8, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.66 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MCSG1 A8 (267517a8): 100mM Tris:HCl pH7.0, 20% (w/v) PEG2000MME, 3mM UDP-glucose, 3mM glucose-6-phosphate, protein conc. 20mg/mL, 20% ethylene glycol cryoprotectant, puck hnk1-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 55408 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.26
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.52 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WTX

2wtx


Resolution: 2→48.28 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1958 3.54 %Random selection
Rwork0.157 ---
obs0.158 55377 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.27 Å2
Refinement stepCycle: LAST / Resolution: 2→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 48 430 3984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073721
X-RAY DIFFRACTIONf_angle_d0.7665056
X-RAY DIFFRACTIONf_dihedral_angle_d15.5392248
X-RAY DIFFRACTIONf_chiral_restr0.054546
X-RAY DIFFRACTIONf_plane_restr0.006668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.21221380.18363759X-RAY DIFFRACTION100
2.05-2.10550.19741460.173778X-RAY DIFFRACTION100
2.1055-2.16740.22261390.16413783X-RAY DIFFRACTION100
2.1674-2.23740.18441350.15473762X-RAY DIFFRACTION100
2.2374-2.31730.18971440.16123799X-RAY DIFFRACTION100
2.3173-2.41010.22391480.16223784X-RAY DIFFRACTION100
2.4101-2.51980.20081450.16723795X-RAY DIFFRACTION100
2.5198-2.65260.21121450.16293793X-RAY DIFFRACTION100
2.6526-2.81880.19971240.17143832X-RAY DIFFRACTION100
2.8188-3.03640.19781270.17393838X-RAY DIFFRACTION100
3.0364-3.34190.1961470.16463837X-RAY DIFFRACTION100
3.3419-3.82530.16711350.14193855X-RAY DIFFRACTION99
3.8253-4.81880.16251350.1273862X-RAY DIFFRACTION98
4.8188-48.29620.15951500.16323942X-RAY DIFFRACTION95
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)
18.91581.1433-1.13936.56620.99849.1970.0030.62430.2574-0.7144-0.19230.1298-0.1175-0.33250.17310.2070.0788-0.09040.33340.03270.264957.4898-31.0189-17.7157
20.54060.2322-0.23090.8101-0.14221.4223-0.04180.00670.077-0.0155-0.04370.194-0.1058-0.37340.05040.15190.0169-0.05510.194-0.03180.222566.097-28.967-6.6623
31.21780.32910.29793.1380.03211.35480.0459-0.02150.02330.0834-0.07830.1404-0.0538-0.13940.03050.1790.0329-0.00450.11520.00340.129384.74-14.4482-22.1933
41.0385-0.0761-0.92440.0901-0.1791.79-0.12610.2004-0.1726-0.19570.0419-0.03370.1966-0.2090.10240.24180.0281-0.05450.0983-0.01610.20780.3492-32.0923-25.0566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 43 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 44 THROUGH 260 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 261 THROUGH 414 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 415 THROUGH 465 )

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