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- PDB-3oi7: Structure of the structure of the H13A mutant of Ykr043C in compl... -

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Basic information

Entry
Database: PDB / ID: 3oi7
TitleStructure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate
ComponentsUncharacterized protein YKR043C
KeywordsHYDROLASE / beta-furanose / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta / sedoheptulose-1 / 7-bisphosphatase / phosphatase
Function / homology
Function and homology information


sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / ribose phosphate biosynthetic process / oxidoreductase activity / nucleus / cytoplasm
Similarity search - Function
: / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OI7 / Sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSinger, A.U. / Xu, X. / Dong, A. / Cui, H. / Clasquin, M.F. / Caudy, A.A. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Riboneogenesis in yeast.
Authors: Clasquin, M.F. / Melamud, E. / Singer, A. / Gooding, J.R. / Xu, X. / Dong, A. / Cui, H. / Campagna, S.R. / Savchenko, A. / Yakunin, A.F. / Rabinowitz, J.D. / Caudy, A.A.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: 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_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YKR043C
B: Uncharacterized protein YKR043C
C: Uncharacterized protein YKR043C
D: Uncharacterized protein YKR043C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,92926
Polymers134,6484
Non-polymers2,28122
Water4,432246
1
A: Uncharacterized protein YKR043C
C: Uncharacterized protein YKR043C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,52214
Polymers67,3242
Non-polymers1,19812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-50 kcal/mol
Surface area22520 Å2
MethodPISA
2
B: Uncharacterized protein YKR043C
D: Uncharacterized protein YKR043C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40712
Polymers67,3242
Non-polymers1,08310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-44 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.559, 74.945, 83.615
Angle α, β, γ (deg.)90.04, 89.92, 77.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 301
2111B1 - 301
3111C1 - 301
4111D1 - 301

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Uncharacterized protein YKR043C


Mass: 33661.906 Da / Num. of mol.: 4 / Mutation: H13A
Source method: isolated from a genetically manipulated source
Details: no TEV cleavage, but limiting amounts of trypsin added during crystallization
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YKR043C / Plasmid: P15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: P36136, fructose-bisphosphatase
#2: Sugar
ChemComp-OI7 / 1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose / 1,7-di-O-phosphono-beta-D-altro-hept-2-ulose / 1,7-di-O-phosphono-D-altro-hept-2-ulose / 1,7-di-O-phosphono-altro-hept-2-ulose


Type: D-saccharide, beta linking / Mass: 370.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H16O13P2

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Non-polymers , 5 types, 264 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes 7.5, 10%Iso-propnal, 22%PEG4K, 4%Glycerol, 0.03 mg/ml trypsin, soaking 10min in well solution w/10mM sedoheptulose. Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 22, 2010 / Details: mirrors
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 69828 / Num. obs: 57671 / % possible obs: 82.6 % / Observed criterion σ(F): -3 / Redundancy: 1.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.88
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 3.02 / Num. unique all: 1286 / % possible all: 36.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3F3K molecule A protein atoms

3f3k


Resolution: 2.4→27.5 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.448 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25996 2567 5.2 %RANDOM
Rwork0.22842 ---
obs0.23007 46894 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.02 Å20.01 Å2
2---0.01 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8392 0 135 246 8773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.96911884
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14951048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25523.2450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.964151488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481593
X-RAY DIFFRACTIONr_chiral_restr0.0910.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026721
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25917
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2540.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.741.55201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56628413
X-RAY DIFFRACTIONr_scbond_it2.7633700
X-RAY DIFFRACTIONr_scangle_it4.7354.53470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2082 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.020.05
2Btight positional0.020.05
3Ctight positional0.020.05
4Dtight positional0.020.05
1Atight thermal0.060.5
2Btight thermal0.060.5
3Ctight thermal0.060.5
4Dtight thermal0.060.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 142 -
Rwork0.269 2861 -
obs-3003 76.16 %

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