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- PDB-3ll4: Structure of the H13A mutant of Ykr043C in complex with fructose-... -

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Basic information

Entry
Database: PDB / ID: 3ll4
TitleStructure of the H13A mutant of Ykr043C in complex with fructose-1,6-bisphosphate
ComponentsUncharacterized protein YKR043C
KeywordsHYDROLASE / fructose-1 / 6-bisphosphatase / 1 / 6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Ykr043C / Saccharomyces cerevisiae / metal-independent / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


sedoheptulose-bisphosphatase activity / sedoheptulose-bisphosphatase / 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
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSinger, A. / Xu, X. / Cui, H. / Dong, A. / Stogios, P.J. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / 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 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,5354
Polymers66,8552
Non-polymers6802
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-21 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.620, 84.022, 101.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 270
2111B1 - 270

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Components

#1: Protein Uncharacterized protein YKR043C


Mass: 33427.434 Da / Num. of mol.: 2 / 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(DE3) / References: UniProt: P36136, fructose-bisphosphatase
#2: Sugar ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then ...Details: resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then soaked in well solution plus 12% Glycerol and 0.1M fructose 1,6 bis-phosphate at room temperature for 10 minutes prior to flash-freezing in liquid N2, 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: Dec 14, 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→31.39 Å / Num. all: 25683 / Num. obs: 25181 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 21.28
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1215 / % possible all: 89.1

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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 entry 3F3K molecule A

3f3k


Resolution: 2.49→31.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.829 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1270 5 %RANDOM
Rwork0.22254 ---
obs0.22468 23890 97.63 %-
all-25160 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.49→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 40 57 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9655943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35323.393224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56715749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4941544
X-RAY DIFFRACTIONr_chiral_restr0.10.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21907
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22961
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6511.52688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13724236
X-RAY DIFFRACTIONr_scbond_it1.83731912
X-RAY DIFFRACTIONr_scangle_it2.8844.51707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2096 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.160.5
LS refinement shellResolution: 2.487→2.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 82 -
Rwork0.278 1582 -
obs-1664 89.08 %
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)
10.9921-0.0848-0.25721.5196-0.36471.0405-0.0677-0.00810.03780.05710.0625-0.0272-0.02810.07010.0052-0.0933-0.00020.0055-0.0881-0.0134-0.0987-6.924415.4061-21.4363
20.902-0.15320.30051.54950.33751.0059-0.0581-0.0035-0.05730.09040.0520.05920.0222-0.06370.0061-0.0988-0.0034-0.005-0.07860.0045-0.0928-34.849913.3262-21.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 263
2X-RAY DIFFRACTION2B3 - 263

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