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- PDB-5uof: Crystal structure of alpha,alpha-trehalose 6-phosphate sythase fr... -

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Basic information

Entry
Database: PDB / ID: 5uof
TitleCrystal structure of alpha,alpha-trehalose 6-phosphate sythase from Burkholderia multivorans
ComponentsAlpha,alpha-trehalose-phosphate synthase (UDP-forming)
KeywordsTRANSFERASE / SSGCID / Burkholderia multivorans / alpha / alpha-trehalose-phosphate synthase / UDP-forming / trehalose biosythesis / 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
SERINE / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of alpha,alpha-trehalose 6-phosphate sythase from Burkholderia multivorans
Authors: Irwin, R.M. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / 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.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,15844
Polymers107,5862
Non-polymers2,57242
Water21,1501174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint92 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.580, 128.920, 85.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 53793.172 Da / Num. of mol.: 2 / Fragment: BumuA.00046.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: otsA, BMULJ_02361 / Plasmid: BumuA.00046.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3KGN3, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus screen, H6: 0.1 M MOPs/HEPES-Na pH 7.5, 10% PEG 8000, 20% ethylene glycol, 0.02 M NaGlu, Ala, Gly, Lys, and Ser: BumuA.00046.b.B1.PS37880 at 18.6 mg/ml: direct cryo: tray 272185 well H6, puck omx7-10

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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-300 / Detector: CCD / Date: Jun 22, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 142053 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.217 % / Biso Wilson estimate: 15.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.094 / Χ2: 0.949 / Net I/σ(I): 14.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.746.3120.5443.45102800.9040.59397.7
1.74-1.796.2950.4424.22100730.9340.48197.8
1.79-1.846.2870.3645.0597980.9510.39798.3
1.84-1.96.270.3035.9495190.9620.3398.1
1.9-1.966.2480.247.492780.9740.26298.4
1.96-2.036.220.2018.6889630.9810.21998.6
2.03-2.116.2060.16610.2786880.9850.18298.6
2.11-2.196.1750.13312.383810.990.14598.8
2.19-2.296.1660.1141480480.9920.12499
2.29-2.46.1820.10215.3677270.9930.11198.9
2.4-2.536.1760.08917.0473790.9950.09799.1
2.53-2.696.2040.07918.7569840.9960.08699.3
2.69-2.876.2390.06820.9365770.9960.07499.5
2.87-3.16.250.05923.7761550.9970.06499.6
3.1-3.46.2490.0527.0656790.9970.05599.7
3.4-3.86.2350.04830.0651800.9970.05399.7
3.8-4.396.2050.04831.5945750.9970.05399.7
4.39-5.386.1330.05332.1539340.9950.05899.7
5.38-7.66.020.05730.7230700.9960.06399.9
7.6-505.4350.0573217650.9950.06398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HXA

5hxa


Resolution: 1.7→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.69
RfactorNum. reflection% reflection
Rfree0.1853 2055 1.45 %
Rwork0.1578 --
obs0.1582 141991 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.38 Å2 / Biso mean: 23.8782 Å2 / Biso min: 6.82 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7226 0 170 1237 8633
Biso mean--42.27 35 -
Num. residues----931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067771
X-RAY DIFFRACTIONf_angle_d0.810538
X-RAY DIFFRACTIONf_chiral_restr0.0541148
X-RAY DIFFRACTIONf_plane_restr0.0061386
X-RAY DIFFRACTIONf_dihedral_angle_d13.54701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.73950.26311320.227912598
1.7395-1.7830.23791290.2119914598
1.783-1.83120.22451300.2031915398
1.8312-1.88510.23031300.1981919498
1.8851-1.94590.24021540.1867918098
1.9459-2.01550.23281250.1767927099
2.0155-2.09620.22641210.1663924098
2.0962-2.19160.18751430.1587928499
2.1916-2.30710.17691360.1522933699
2.3071-2.45170.191410.1545932899
2.4517-2.6410.20271500.1518933699
2.641-2.90670.18011430.1543942799
2.9067-3.32720.1891180.14799493100
3.3272-4.19160.14581480.13159564100
4.1916-500.15251550.14699861100
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)
11.73360.20280.00890.6998-0.53891.7472-0.03920.207-0.1342-0.0478-0.0745-0.16240.11780.50160.07970.1048-0.00710.00040.28250.03190.168227.83126.79213.647
20.60210.32560.27721.0010.50831.3318-0.0110.0643-0.0039-0.00230.0144-0.0754-0.01850.0799-0.0130.08030.0216-0.0060.09530.02570.10868.24923.0763.133
30.56890.1987-0.00720.8101-0.07960.87220.03360.0445-0.00330.0382-0.0493-0.0703-0.05920.08780.00340.08530.0010.00380.10720.01570.07696.8923.282-0.361
41.9036-0.0904-0.31120.75780.24780.9795-0.01470.0685-0.06620.05840.02260.0511-0.004-0.06570.00770.09720.016-0.00450.10.01770.0965-16.78833.53729.273
50.9136-0.3490.24420.8298-0.2740.8350.0276-0.0419-0.07140.0069-0.00390.02610.0412-0.0511-0.02140.097-0.0129-0.00270.0769-0.00060.08472.29225.65646.745
629.92645.07647.35684.283320.7358-1.3117-0.0688-0.0098-0.8001-0.67-0.2261.14820.04590.7556-0.0098-0.11240.76960.01930.6317-12.72127.87811.816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:196 )A8 - 196
2X-RAY DIFFRACTION2( CHAIN A AND RESID 197:313 )A197 - 313
3X-RAY DIFFRACTION3( CHAIN A AND RESID 314:478 )A314 - 478
4X-RAY DIFFRACTION4( CHAIN B AND RESID 9:225 )B9 - 225
5X-RAY DIFFRACTION5( CHAIN B AND RESID 226:469 )B226 - 469
6X-RAY DIFFRACTION6( CHAIN B AND RESID 501:501 )B501

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