[English] 日本語
Yorodumi
- PDB-3mbf: Crystal structure of fructose bisphosphate aldolase from Encephal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mbf
TitleCrystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / (SSGCID) / ALDOLASE / Glycolysis / Schiff base
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.37 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi.
Authors: Gardberg, A. / Sankaran, B. / Davies, D. / Bhandari, J. / Staker, B. / Stewart, L.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 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 / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6032
Polymers38,2631
Non-polymers3401
Water1,71195
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2064
Polymers76,5262
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3360 Å2
ΔGint-17 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.460, 135.820, 61.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-411-

HOH

-
Components

#1: Protein Fructose-bisphosphate aldolase


Mass: 38263.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU01_0240 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SSM8, fructose-bisphosphate aldolase
#2: Sugar ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BASED ON PACT SCREEN CONDITION F10 WITHOUT NAKHPO4: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 20 MM FRUCTOSE 1,6-BISPHOSPHATE, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.37→28.03 Å / Num. all: 21111 / Num. obs: 21046 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.35
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1557 / % possible all: 99.6

-
Processing

Software
NameClassification
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3MDB

3mdb


Resolution: 2.37→28.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.8 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1022 4.9 %To match 3MBD (random)
Rwork0.165 ---
obs0.167 20970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---0.44 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.37→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 19 95 2731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222708
X-RAY DIFFRACTIONr_bond_other_d0.0010.021880
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9873659
X-RAY DIFFRACTIONr_angle_other_deg0.934589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60623.947114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3315493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3071518
X-RAY DIFFRACTIONr_chiral_restr0.0830.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.51675
X-RAY DIFFRACTIONr_mcbond_other0.1691.5698
X-RAY DIFFRACTIONr_mcangle_it1.3622689
X-RAY DIFFRACTIONr_scbond_it2.3531033
X-RAY DIFFRACTIONr_scangle_it3.8714.5966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 92 -
Rwork0.215 1442 -
obs--99.35 %
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)
115.3371.95284.7245.6215.41015.82770.3961-0.633-0.90360.86150.1291-0.47820.91290.1291-0.52530.2030.075-0.07790.10190.06990.1122-0.45-26.8763.888
22.471-0.0426-0.4531.72940.28121.63430.0159-0.1881-0.17890.18650.0120.30380.0926-0.1255-0.02790.1096-0.06360.03060.07710.05920.1667-26.029-24.3594.48
30.6847-0.0112-0.20431.3798-0.15321.03260.0367-0.0280.03220.12630.00220.0711-0.1038-0.0076-0.03880.0882-0.01070.00260.04880.00660.0828-12.689-9.844-3.556
41.36830.07810.26881.1107-0.12081.13280.01750.1528-0.0985-0.09790.04770.10550.0562-0.0393-0.06520.0896-0.0198-0.02290.0489-0.00260.0996-13.066-20.47-17.564
51.0793-0.4796-1.63180.99110.40662.1878-0.11370.0629-0.21580.130.11780.36330.2745-0.1903-0.00410.1588-0.0925-0.05550.11720.05820.3338-29.764-31.858-6.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 15
2X-RAY DIFFRACTION2A16 - 98
3X-RAY DIFFRACTION3A99 - 183
4X-RAY DIFFRACTION4A184 - 290
5X-RAY DIFFRACTION5A291 - 338

+
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