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- PDB-5hvo: Structure of Aspergillus fumigatus trehalose-6-phosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 5hvo
TitleStructure of Aspergillus fumigatus trehalose-6-phosphate synthase B in complex with UDP and validoxylamine A
ComponentsAlpha,alpha-trehalose-phosphate synthase (UDP-forming)
KeywordsTRANSFERASE / trehalose-6-phosphate synthase
Function / homology
Function and homology information


trehalose synthase activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / cellular response to heat / carbohydrate metabolic process / nucleotide binding
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
URIDINE-5'-DIPHOSPHATE / Chem-VDM / Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 2
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.467 Å
AuthorsMiao, Y. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1P01AI104533-01A1 United States
CitationJournal: MBio / Year: 2017
Title: Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design.
Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Maskarinec, S.A. / Liu, J. / Lee, R.E. / Perfect, J.R. / Brennan, R.G.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)218,43112
Polymers215,4734
Non-polymers2,9588
Water3,459192
1
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)109,2166
Polymers107,7372
Non-polymers1,4794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-27 kcal/mol
Surface area36340 Å2
MethodPISA
2
C: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
D: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2166
Polymers107,7372
Non-polymers1,4794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-28 kcal/mol
Surface area36270 Å2
MethodPISA
3
A: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
B: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules

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)218,43112
Polymers215,4734
Non-polymers2,9588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area15000 Å2
ΔGint-75 kcal/mol
Surface area68370 Å2
MethodPISA
4
C: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
D: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)218,43112
Polymers215,4734
Non-polymers2,9588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564x,-y+1,-z-11
Buried area14720 Å2
ΔGint-76 kcal/mol
Surface area68370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.276, 130.581, 184.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 53868.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_2G04010 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WHW0, 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: Chemical
ChemComp-VDM / (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL / VALIDOXYLAMINE


Mass: 335.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H25NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M lithium sulfate, 0.1 M Tris, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 74743 / % possible obs: 97.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.054 / Rrim(I) all: 0.12 / Χ2: 0.989 / Net I/av σ(I): 17.251 / Net I/σ(I): 7.5 / Num. measured all: 371828
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.46-2.54.30.68237240.640.370.780.59498.9
2.5-2.554.50.61837330.7370.3260.7020.59998.8
2.55-2.64.70.61937260.760.3210.6990.63298.5
2.6-2.654.90.59137710.7710.3020.6660.63698.9
2.65-2.7150.51737080.820.2610.5810.66898.4
2.71-2.7750.46237020.8770.2310.5180.67498.7
2.77-2.845.10.38437330.9130.1910.4310.68998.3
2.84-2.925.10.31437260.940.1560.3520.75598.4
2.92-35.10.25337600.9520.1260.2840.79698.3
3-3.15.10.20337170.9710.1010.2270.88798.1
3.1-3.215.10.16737040.9790.0830.1860.98497.9
3.21-3.345.10.13537460.9870.0670.1511.07297.8
3.34-3.495.10.11237040.990.0550.1251.16897.6
3.49-3.675.10.08837300.9920.0440.0991.20297.5
3.67-3.95.10.07437300.9940.0370.0831.28497.4
3.9-4.215.10.06937280.9950.0340.0771.52896.9
4.21-4.635.10.07537450.9930.0370.0841.63396.6
4.63-5.35.10.06837190.9930.0330.0761.35396.3
5.3-6.675.10.06137710.9960.030.0691.21895.8
6.67-504.80.07338660.9880.0370.0821.22493.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.467→39.828 Å / FOM work R set: 0.7969 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1999 2.68 %
Rwork0.2002 72686 -
obs0.2012 74685 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.93 Å2 / Biso mean: 51.77 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 2.467→39.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14584 0 336 192 15112
Biso mean--49.28 48.42 -
Num. residues----1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815142
X-RAY DIFFRACTIONf_angle_d1.20520529
X-RAY DIFFRACTIONf_chiral_restr0.052267
X-RAY DIFFRACTIONf_plane_restr0.0072582
X-RAY DIFFRACTIONf_dihedral_angle_d14.3275501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4667-2.52830.34631150.26324172428778
2.5283-2.59670.26331440.23355249539399
2.5967-2.67310.28141460.22875279542599
2.6731-2.75940.33091440.22935280542499
2.7594-2.85790.28851440.23315222536699
2.8579-2.97230.27811450.23135268541398
2.9723-3.10760.28711450.22165238538398
3.1076-3.27130.20411450.21725274541998
3.2713-3.47620.23791430.20865237538098
3.4762-3.74440.24191450.19315261540698
3.7444-4.12090.21181450.18495260540597
4.1209-4.71630.19961440.17475260540497
4.7163-5.93890.2141460.1925307545396
5.9389-39.8330.23261480.1845379552794

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