[English] 日本語
Yorodumi
- PDB-1up4: Structure of the 6-phospho-beta glucosidase from Thermotoga marit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1up4
TitleStructure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.85 Angstrom resolution in the monoclinic form
Components6-PHOSPHO-BETA-GLUCOSIDASE
KeywordsHYDROLASE / 6-PHOSPHO-BETA-GLUCOSIDASE / FAMILY4 HYDROLASE / NAD-DEPENDENT
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / methyl beta-D-glucoside 6-phosphate glucohydrolase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-phospho-beta-glucosidase BglT
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.85 Å
AuthorsVarrot, A. / Yip, V. / Withers, S.G. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Nad+ and Metal-Ion Dependent Hydrolysis by Family 4 Glycosidases: Structural Insight Into Specificity for Phospho-Beta-D-Glucosides
Authors: Varrot, A. / Yip, V.L. / Li, Y. / Rajan, S.S. / Yang, X. / Anderson, W.F. / Thompson, J. / Withers, S.G. / Davies, G.J.
History
DepositionSep 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 6-PHOSPHO-BETA-GLUCOSIDASE
B: 6-PHOSPHO-BETA-GLUCOSIDASE
C: 6-PHOSPHO-BETA-GLUCOSIDASE
D: 6-PHOSPHO-BETA-GLUCOSIDASE
E: 6-PHOSPHO-BETA-GLUCOSIDASE
F: 6-PHOSPHO-BETA-GLUCOSIDASE
G: 6-PHOSPHO-BETA-GLUCOSIDASE
H: 6-PHOSPHO-BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)384,1768
Polymers384,1768
Non-polymers00
Water2,252125
1
A: 6-PHOSPHO-BETA-GLUCOSIDASE
B: 6-PHOSPHO-BETA-GLUCOSIDASE
C: 6-PHOSPHO-BETA-GLUCOSIDASE
D: 6-PHOSPHO-BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)192,0884
Polymers192,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: 6-PHOSPHO-BETA-GLUCOSIDASE
F: 6-PHOSPHO-BETA-GLUCOSIDASE
G: 6-PHOSPHO-BETA-GLUCOSIDASE
H: 6-PHOSPHO-BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)192,0884
Polymers192,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.048, 188.315, 125.628
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 217
2112B1 - 217
3112C1 - 217
4112D1 - 217
5112E1 - 217
6112F1 - 217
7112G1 - 217
8112H1 - 217
1212A223 - 283
2212B223 - 283
3212C223 - 283
4212D223 - 283
5212E223 - 283
6212F223 - 283
7212G223 - 283
8212H223 - 283
1312A293 - 415
2312B293 - 415
3312C293 - 415
4312D293 - 415
5312E293 - 415
6312F293 - 415
7312G293 - 415
8312H293 - 415

NCS oper:
IDCodeMatrixVector
1given(-0.28575, 0.16821, -0.94343), (0.14315, -0.96594, -0.21558), (-0.94755, -0.19666, 0.25193)86.62768, 114.87262, 84.35545
2given(0.23181, -0.4613, 0.85643), (-0.45289, -0.83035, -0.32467), (0.8609, -0.31261, -0.4014)-5.19723, 131.72482, 77.86082
3given(-0.95038, 0.29885, 0.08646), (0.29871, 0.79891, 0.52203), (0.08693, 0.52195, -0.84853)35.57854, -29.827, 82.82382
4given(0.92493, -0.14532, 0.35126), (0.20881, 0.96638, -0.15002), (-0.31765, 0.2121, 0.92418)28.81234, 9.4414, -79.08702
5given(0.07811, -0.00144, -0.99694), (0.00236, -1, 0.00163), (-0.99694, -0.00249, -0.07811)155.02489, 126.36591, 36.24427
6given(-0.15129, -0.29986, 0.94191), (-0.50555, -0.79535, -0.33441), (0.84943, -0.52677, -0.03127)63.86448, 160.55737, 18.39849
7given(-0.84121, 0.45221, -0.29644), (0.28578, 0.83723, 0.46623), (0.45902, 0.30748, -0.83352)77.50006, -35.10963, -3.24922

-
Components

#1: Protein
6-PHOSPHO-BETA-GLUCOSIDASE /


Mass: 48021.973 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: SYNTHETIC GENE / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9X108, EC: 3.2.1.6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growpH: 4.6
Details: 200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 5% PEG 4000. PROTEIN AT 5 MG/ML

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorDate: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. obs: 103065 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.3
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.4 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.85→40 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.59 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND ATOMS HAVE BEEN GIVEN AN OCCUPANCY OF 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5153 5 %RANDOM
Rwork0.196 ---
obs0.198 97911 99.6 %-
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: 21.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å22.05 Å2
2--1.74 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26200 0 0 125 26325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02226716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.96936001
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54153206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.24008
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.211879
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2715
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4111.516023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.959225963
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.147310693
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.424.510038
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1564tight positional0.050.05
2B1564tight positional0.050.05
3C1564tight positional0.040.05
4D1564tight positional0.050.05
5E1564tight positional0.040.05
6F1564tight positional0.050.05
7G1564tight positional0.060.05
8H1564tight positional0.040.05
1A1607medium positional0.50.5
2B1607medium positional0.590.5
3C1607medium positional0.490.5
4D1607medium positional0.590.5
5E1607medium positional0.520.5
6F1607medium positional0.530.5
7G1607medium positional0.550.5
8H1607medium positional0.560.5
1A1564tight thermal0.090.5
2B1564tight thermal0.10.5
3C1564tight thermal0.070.5
4D1564tight thermal0.070.5
5E1564tight thermal0.080.5
6F1564tight thermal0.070.5
7G1564tight thermal0.090.5
8H1564tight thermal0.080.5
1A1607medium thermal0.672
2B1607medium thermal0.792
3C1607medium thermal0.572
4D1607medium thermal0.582
5E1607medium thermal0.622
6F1607medium thermal0.652
7G1607medium thermal0.672
8H1607medium thermal0.662
LS refinement shellResolution: 2.85→2.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 338
Rwork0.229 6863

+
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