[English] 日本語
Yorodumi
- PDB-1vjt: Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vjt
TitleCrystal structure of Alpha-glucosidase (TM0752) from Thermotoga maritima at 2.50 A resolution
Componentsalpha-glucosidase
KeywordsHYDROLASE / TM0752 / ALPHA-GLUCOSIDASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding
Similarity search - Function
: / : / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / : / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga maritima at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Remark 600HETEROGEN THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2632
Polymers57,5991
Non-polymers6631
Water86548
1
A: alpha-glucosidase
hetero molecules

A: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5254
Polymers115,1992
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Unit cell
Length a, b, c (Å)75.722, 79.815, 89.222
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein alpha-glucosidase


Mass: 57599.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0752 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZL1, EC: 3.2.1.139
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.38 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.1
Details: 0.2M tri-lithium citrate tetrahydrate, 20% PEG-3350, pH 8.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00000, 0.979340, 0.979206
DetectorType: APS / Detector: CCD / Date: Aug 8, 2003
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979341
30.9792061
ReflectionResolution: 2.5→50 Å / Num. obs: 15162 / % possible obs: 83.34 % / Redundancy: 3.12 % / Biso Wilson estimate: 44.23 Å2 / Rsym value: 0.057 / Net I/σ(I): 19.08
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.03 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 758 / Rsym value: 0.264 / % possible all: 42.11

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RESOLVEmodel building
REFMAC5.2.0001refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→43.64 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.878 / SU B: 22.539 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.362
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF THE ACTIVE SITE RESIDUES SER10 AND PHE13.
RfactorNum. reflection% reflectionSelection details
Rfree0.25602 754 5 %RANDOM
Rwork0.1944 ---
obs0.19754 14406 83.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.232 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.36 Å2
2---0.33 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 36 48 3956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224018
X-RAY DIFFRACTIONr_bond_other_d0.0010.023595
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9475451
X-RAY DIFFRACTIONr_angle_other_deg0.80438355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31223.582201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78815698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3481531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_nbd_refined0.1970.2874
X-RAY DIFFRACTIONr_nbd_other0.1720.23685
X-RAY DIFFRACTIONr_nbtor_other0.0840.22338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.28
X-RAY DIFFRACTIONr_mcbond_it0.571.52546
X-RAY DIFFRACTIONr_mcbond_other0.0821.5946
X-RAY DIFFRACTIONr_mcangle_it0.81623812
X-RAY DIFFRACTIONr_scbond_it1.10431881
X-RAY DIFFRACTIONr_scangle_it1.7024.51639
LS refinement shellResolution: 2.495→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 19 3.58 %
Rwork0.273 512 -
Refinement TLS params.Method: refined / Origin x: 59.5753 Å / Origin y: 9.3396 Å / Origin z: 21.7988 Å
111213212223313233
T-0.0468 Å2-0.0034 Å2-0.0251 Å2--0.0221 Å2-0.0208 Å2---0.0112 Å2
L0.2988 °2-0.1978 °2-0.0578 °2-0.9307 °2-0.2684 °2--1.2814 °2
S0.0067 Å °0.1826 Å °-0.0399 Å °-0.1821 Å °0.0214 Å °0.042 Å °0.0202 Å °-0.0437 Å °-0.0281 Å °
Refinement TLS groupSelection: ALL

+
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