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- PDB-3lg2: A Ykr043C/ fructose-1,6-bisphosphate product complex following li... -

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Basic information

Entry
Database: PDB / ID: 3lg2
TitleA Ykr043C/ fructose-1,6-bisphosphate product complex following ligand soaking
ComponentsUncharacterized protein YKR043C
KeywordsHYDROLASE / metal-independent / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
PHOSPHATE ION / Sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSinger, A. / Xu, X. / Cui, H. / Dong, A. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae.
Authors: Kuznetsova, E. / Xu, L. / Singer, A. / Brown, G. / Dong, A. / Flick, R. / Cui, H. / Cuff, M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 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)135,67612
Polymers134,9164
Non-polymers7608
Water724
1
A: Uncharacterized protein YKR043C
B: Uncharacterized protein YKR043C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8386
Polymers67,4582
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-55 kcal/mol
Surface area21880 Å2
MethodPISA
2
C: Uncharacterized protein YKR043C
D: Uncharacterized protein YKR043C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8386
Polymers67,4582
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-55 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.302, 83.385, 104.685
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 302
2112B1 - 302
3112C1 - 302
4112D1 - 302

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Components

#1: Protein
Uncharacterized protein YKR043C


Mass: 33728.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YKR043C / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36136, fructose-bisphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD with 0.03 mg/ml trypsin in the protein. Soak with 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD and 100 mM Fructose-1,6-bisphosphate for 2 hours, ...Details: 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD with 0.03 mg/ml trypsin in the protein. Soak with 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD and 100 mM Fructose-1,6-bisphosphate for 2 hours, 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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2009 / Details: Mirrors
RadiationMonochromator: VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 48678 / Num. obs: 44466 / % possible obs: 91.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.9 / % possible all: 93.3

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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: 3F3K molecule A

3f3k


Resolution: 2.6→43.35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU B: 27.974 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 2008 5.1 %RANDOM
Rwork0.22003 ---
obs0.22258 37178 91.17 %-
all-39186 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.02 Å2
2---0.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8688 0 40 4 8732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.95712088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29351072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53523.504468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.846151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg171588
X-RAY DIFFRACTIONr_chiral_restr0.1080.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026920
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.24243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.26012
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1076tight positional0.050.05
2B1076tight positional0.050.05
3C1076tight positional0.050.05
4D1076tight positional0.050.05
1A1106medium positional1.110.5
2B1106medium positional1.110.5
3C1106medium positional1.090.5
4D1106medium positional1.10.5
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 160 -
Rwork0.337 2780 -
obs--93.24 %

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