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- PDB-3pt1: Structure of DUF89 from Saccharomyces cerevisiae co-crystallized ... -

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Basic information

Entry
Database: PDB / ID: 3pt1
TitleStructure of DUF89 from Saccharomyces cerevisiae co-crystallized with F6P.
ComponentsUPF0364 protein YMR027W
KeywordsHYDROLASE / alpha/beta fold / carbohydrate phosphatase / F6P binding
Function / homology
Function and homology information


fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #60 / Damage-control phosphatase ARMT1 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Transcription Elongation Factor S-II; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / Damage-control phosphatase YMR027W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsPetit, P. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A.F.
CitationJournal: To be Published
Title: Structure and activity of a DUF89 protein from Saccharomyces cerevisiae revealed a novel family of carbohydrate phosphatases
Authors: Brown, G. / Xu, X. / Petit, P. / Cui, H. / Flick, R. / Cuff, M. / Savchenko, A. / Yakunin, A.F.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0364 protein YMR027W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0404
Polymers54,6641
Non-polymers3773
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.320, 108.650, 88.080
Angle α, β, γ (deg.)90.00, 96.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

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Components

#1: Protein UPF0364 protein YMR027W


Mass: 54663.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YM9711.17, YMR027W / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04371
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→34.07 Å / Num. obs: 48080 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 19.8
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6928 / Rsym value: 0.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.773→29.891 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 2387 5.08 %RANDOM
Rwork0.1562 ---
obs0.158 46980 97.53 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.814 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.466 Å2-0 Å20.6988 Å2
2---5.5365 Å20 Å2
3----3.9295 Å2
Refinement stepCycle: LAST / Resolution: 1.773→29.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 23 336 4073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073848
X-RAY DIFFRACTIONf_angle_d1.045220
X-RAY DIFFRACTIONf_dihedral_angle_d16.0851406
X-RAY DIFFRACTIONf_chiral_restr0.072575
X-RAY DIFFRACTIONf_plane_restr0.004658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.773-1.83640.27992420.24364174X-RAY DIFFRACTION92
1.8364-1.90990.22052220.18344290X-RAY DIFFRACTION95
1.9099-1.99680.20362290.15654368X-RAY DIFFRACTION96
1.9968-2.1020.19872370.1474426X-RAY DIFFRACTION97
2.102-2.23370.18532360.13914487X-RAY DIFFRACTION98
2.2337-2.40610.19182320.14734533X-RAY DIFFRACTION99
2.4061-2.64810.2232410.164554X-RAY DIFFRACTION99
2.6481-3.03090.19042170.16344591X-RAY DIFFRACTION100
3.0309-3.81740.16842550.15124569X-RAY DIFFRACTION100
3.8174-29.89560.17912760.14894601X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.4329 Å / Origin y: -0.8381 Å / Origin z: -21.103 Å
111213212223313233
T0.0551 Å2-0.013 Å2-0.0138 Å2-0.0772 Å2-0.0015 Å2--0.0534 Å2
L0.4507 °20.1282 °2-0.1894 °2-1.0944 °20.0572 °2--0.3767 °2
S0.0206 Å °-0.0011 Å °-0.0018 Å °-0.0471 Å °-0.0292 Å °0.053 Å °-0.0009 Å °0.0079 Å °0.0066 Å °
Refinement TLS groupSelection details: all

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