[English] 日本語
Yorodumi
- PDB-4go8: Crystal Structure of the TREHALULOSE SYNTHASE MUTB, MUTANT A258V,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4go8
TitleCrystal Structure of the TREHALULOSE SYNTHASE MUTB, MUTANT A258V, in complex with TRIS
ComponentsSucrose isomerase
KeywordsISOMERASE / MUTANT ENZYME / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING
Function / homology
Function and homology information


isomerase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas mesoacidophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsLipski, A. / Haser, R. / Aghajari, N.
CitationJournal: To be Published / Year: 2013
Title: Crystal structure of MUTB A258V mutant in complex with TRIS
Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sucrose isomerase
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2586
Polymers127,9342
Non-polymers3244
Water19,1501063
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1293
Polymers63,9671
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1293
Polymers63,9671
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.51, 71.31, 81.53
Angle α, β, γ (deg.)68.04, 72.72, 70.10
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63966.902 Da / Num. of mol.: 2 / Fragment: MUTB fragment, UNP residues 28-584 / Mutation: A258V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Gene: mutB / Plasmid: PHWG660.7 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, EC: 5.4.11.99
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 12%(w/v) PEG20000, 0.01M L-Cysteine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97559 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: Toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97559 Å / Relative weight: 1
ReflectionResolution: 2.15→14.82 Å / Num. all: 66682 / Num. obs: 62687 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.46 / Num. unique all: 11394 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJB

1zjb


Resolution: 2.15→14.82 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3184 5.08 %RANDOM
Rwork0.1904 ---
obs0.194 62658 94.5 %-
all-62658 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8900 0 18 1063 9981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039214
X-RAY DIFFRACTIONf_angle_d0.66512546
X-RAY DIFFRACTIONf_dihedral_angle_d10.8893313
X-RAY DIFFRACTIONf_chiral_restr0.0521282
X-RAY DIFFRACTIONf_plane_restr0.0031653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.1820.28431260.2085258494
2.182-2.2160.27551310.2008258794
2.216-2.25220.29941500.2078254094
2.2522-2.29090.26081430.2104251492
2.2909-2.33240.29221140.2039259294
2.3324-2.37710.30221330.199259495
2.3771-2.42540.26011360.1903262595
2.4254-2.47790.25531250.1883260695
2.4779-2.53530.2521470.1979258794
2.5353-2.59830.28141280.2009258895
2.5983-2.66820.30011490.2087261596
2.6682-2.74620.30231370.206263095
2.7462-2.83430.23781400.186258196
2.8343-2.93480.23981520.1797262296
2.9348-3.05140.24761520.1877258195
3.0514-3.18890.29511380.1877261495
3.1889-3.35520.21341620.1775258895
3.3552-3.56270.22461380.1778262695
3.5627-3.83340.23591430.1719252294
3.8334-4.21110.20181220.1642257793
4.2111-4.80220.21731370.1787250492
4.8022-5.98340.22371530.1945259295
5.9834-14.82450.23491280.2229260595

+
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