[English] 日本語
Yorodumi
- PDB-3t08: E. coli (LacZ) beta-galactosidase (S796A) IPTG complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t08
TitleE. coli (LacZ) beta-galactosidase (S796A) IPTG complex
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Dynampic Loop Conformation / Ser-796 / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / BETA SUPERSANDWICH / GLYCOSIDASE
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsJancewicz, L.J. / Wheatley, R.W. / Sutendra, G. / Lee, M. / Fraser, M. / Huber, R.E.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: Ser-796 of Beta-Galactosidase (E. coli) Plays a Key Role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop
Authors: Jancewicz, L.J. / Wheatley, R.W. / Sutendra, G. / Lee, M. / Fraser, M.E. / Huber, R.E.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name / _software.version
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,929101
Polymers478,9114
Non-polymers7,01897
Water55,7563095
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37570 Å2
ΔGint-86 kcal/mol
Surface area137510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.160, 161.590, 202.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Beta-galactosidase / / Beta-gal / Lactase


Mass: 119727.758 Da / Num. of mol.: 4 / Fragment: Unp residues 10-1024 / Mutation: S796A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0344, JW0335, lacZ / Plasmid: pBAD/HIS/LacZ / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P00722, beta-galactosidase
#4: Sugar
ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside / Isopropyl β-D-1-thiogalactopyranoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 3188 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3095 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8-10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 30, 2006 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2→200 Å / Num. all: 288591 / Num. obs: 288591 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.02 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.29 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 0.9 / Num. unique all: 10314 / % possible all: 62.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→74.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.22272 4166 1.4 %
Rwork0.17467 --
all0.17535 284340 -
obs0.17535 284340 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2---0.06 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2→74.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32624 0 366 3095 36085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02133854
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.93346027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15754042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57723.7491750
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18155167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.09815263
X-RAY DIFFRACTIONr_chiral_restr0.0720.24861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126599
X-RAY DIFFRACTIONr_mcbond_it1.881220314
X-RAY DIFFRACTIONr_mcangle_it2.8662.532734
X-RAY DIFFRACTIONr_scbond_it4.1673.513540
X-RAY DIFFRACTIONr_scangle_it5.8114.513293
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 215 -
Rwork0.278 15313 -
obs--100 %

+
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