[English] 日本語
Yorodumi
- PDB-3f3k: The structure of uncharacterized protein YKR043C from Saccharomyc... -

+
Open data


ID or keywords:

Loading...

-
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 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
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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more