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- PDB-3f3k: The structure of uncharacterized protein YKR043C from Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 3f3k
TitleThe structure of uncharacterized protein YKR043C from Saccharomyces cerevisiae.
ComponentsUncharacterized protein YKR043C
Keywordsstructural genomics / unknown function / Saccharomyces cerevisiae / 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
Sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsCuff, M. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, 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
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5768
Polymers61,0242
Non-polymers5536
Water16,916939
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-25 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.037, 86.277, 100.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit is experimentally unknown.

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Components

#1: Protein Uncharacterized protein YKR043C


Mass: 30511.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YKR043C / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36136
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Li3Citrate, 16% PEG 3350, 4%MPD, 10% Glycerol, Trypsin 1/10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948,0.97931
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979311
ReflectionResolution: 1.75→50 Å / Num. all: 72754 / Num. obs: 72754 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.074 / Χ2: 1.694 / Net I/σ(I): 40.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.265 / Num. unique all: 3587 / Χ2: 0.839 / % possible all: 98.4

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.75 Å / D res low: 50 Å / FOM : 0.387 / FOM acentric: 0.405 / FOM centric: 0.17 / Reflection: 72654 / Reflection acentric: 67134 / Reflection centric: 5520
Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.410.20.100671345520
20.960.9410.614.20.370.28670775515
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
111.24-501.2510.20.20019196
16.33-11.241.5610.30.2001039246
14.41-6.331.310.30.2002638422
13.38-4.411.0410.20.2004972603
12.74-3.381.310.20.1008078792
12.31-2.741.4410.20.10011955966
11.99-2.311.4110.20.100165561121
11.75-1.991.7310.10.100217051274
211.24-500.940.8712.417.60.760.5319195
26.33-11.240.850.7610.412.30.850.751039246
24.41-6.330.880.8111.313.70.720.512638422
23.38-4.410.930.9213.1180.520.34972602
22.74-3.380.930.9310.213.20.530.338076792
22.31-2.740.950.969.213.30.450.2511949965
21.99-2.310.980.9810.113.60.310.2165451121
21.75-1.990.990.9911.114.70.20.14216671272
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.82862-0.517-0.845-0.0870
2Se14.75583-0.637-1.153-0.0880
3Se14.34521-0.656-0.852-0.0730
4Se12.6175-0.498-1.146-0.0740
5Se14.48561-0.313-1.248-0.1120
6Se14.9109-0.841-0.75-0.1140
7Se-267.51013-0.329-1.156-0.0870
8Se13.61214-0.517-0.845-0.087-0.111
9Se14.27805-0.637-1.153-0.088-0.107
10Se12.34448-0.656-0.852-0.073-0.059
11Se9.4961-0.498-1.146-0.073-0.06
12Se14.93218-0.313-1.248-0.111-0.052
13Se17.17247-0.841-0.75-0.114-0.053
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.24-500.4530.5530.25528719196
6.33-11.240.5830.6350.36212851039246
4.41-6.330.5650.6030.32630602638422
3.38-4.410.50.5320.23255754972603
2.74-3.380.5030.5310.20988708078792
2.31-2.740.4490.4720.1671292111955966
1.99-2.310.3670.3840.11617677165561121
1.75-1.990.2610.2730.0722979217051274
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 72654
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.22-10054.10.714515
6.61-9.2250.50.81862
5.42-6.6151.50.81117
4.71-5.4248.40.8321314
4.22-4.7149.10.8561482
3.85-4.2251.90.8341615
3.57-3.8555.40.8341762
3.34-3.5756.50.8261891
3.15-3.3453.50.8242022
2.99-3.1551.10.8322138
2.85-2.9950.80.8462232
2.73-2.8552.30.8462358
2.62-2.7351.70.8412420
2.53-2.62510.8552542
2.44-2.5351.20.8582621
2.37-2.44530.8612714
2.3-2.3752.20.8542794
2.23-2.354.60.8612873
2.17-2.2354.70.8692948
2.12-2.1755.70.8553037
2.07-2.12590.8563093
2.02-2.07600.8563190
1.98-2.0259.40.8523220
1.93-1.9862.20.853311
1.89-1.9360.50.8553361
1.86-1.8963.10.8423444
1.82-1.8664.20.823479
1.79-1.8266.70.7953557
1.75-1.7970.50.7224742

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→43.15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.146 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.901 / SU B: 2.901 / SU ML: 0.043 / SU R Cruickshank DPI: 0.086 / SU Rfree: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3660 5 %RANDOM
Rwork0.141 ---
all0.143 72653 --
obs0.143 72653 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.51 Å2 / Biso mean: 15.734 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.5 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 36 939 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214511
X-RAY DIFFRACTIONr_bond_other_d0.0010.023184
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9596115
X-RAY DIFFRACTIONr_angle_other_deg0.88237687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94723.305236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95115779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631548
X-RAY DIFFRACTIONr_chiral_restr0.0940.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02956
X-RAY DIFFRACTIONr_mcbond_it0.7211.52692
X-RAY DIFFRACTIONr_mcbond_other0.2151.51092
X-RAY DIFFRACTIONr_mcangle_it1.33424369
X-RAY DIFFRACTIONr_scbond_it2.27631819
X-RAY DIFFRACTIONr_scangle_it3.8024.51746
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 272 -
Rwork0.169 4983 -
all-5255 -
obs--97.06 %
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)
10.6490.04070.19730.55440.13210.78160.0395-0.02780.0366-0.0187-0.05110.0271-0.0744-0.04210.01150.01470.00160.00290.0072-0.00450.020634.644814.184.0101
20.61150.003-0.10310.4526-0.05170.64170.0359-0.0213-0.0221-0.02-0.0505-0.03220.04980.03330.01470.01170.0014-0.0060.0080.00740.019436.5597-14.13873.9271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 263
2X-RAY DIFFRACTION2B2 - 263

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