[English] 日本語
Yorodumi
- PDB-5c3m: Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c3m
TitleCrystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus
ComponentsPutative 6-phospho-beta-glucosidase
KeywordsHYDROLASE / Glycoside Hydrolase / Manganese / 6-phospho-glucosidase
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase 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
: / Putative 6-phospho-beta-glucosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.059 Å
AuthorsCohen, T. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus
Authors: Cohen, T. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative 6-phospho-beta-glucosidase
B: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water1,63991
1
A: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
hetero molecules

A: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9320 Å2
ΔGint-58 kcal/mol
Surface area59720 Å2
MethodPISA
2
B: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules

B: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area9510 Å2
ΔGint-63 kcal/mol
Surface area58990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.324, 83.198, 151.372
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Putative 6-phospho-beta-glucosidase


Mass: 49322.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan4C / Production host: Escherichia coli (E. coli) / References: UniProt: W8R9V4, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 16% PEG 8K, 0.1M CHES buffer pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 39747 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 3.06→3.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S6Y

1s6y


Resolution: 3.059→46.603 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3061 1964 4.94 %
Rwork0.2295 --
obs0.2334 39747 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.059→46.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12399 0 4 91 12494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112639
X-RAY DIFFRACTIONf_angle_d1.24917187
X-RAY DIFFRACTIONf_dihedral_angle_d16.0474616
X-RAY DIFFRACTIONf_chiral_restr0.0561991
X-RAY DIFFRACTIONf_plane_restr0.0082237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.059-3.13540.46461380.3312434X-RAY DIFFRACTION91
3.1354-3.22020.34171560.29982648X-RAY DIFFRACTION97
3.2202-3.31490.38651370.28062692X-RAY DIFFRACTION99
3.3149-3.42190.3861130.27682683X-RAY DIFFRACTION100
3.4219-3.54410.36811480.27272699X-RAY DIFFRACTION100
3.5441-3.6860.3741450.26842718X-RAY DIFFRACTION100
3.686-3.85370.37971310.24312727X-RAY DIFFRACTION100
3.8537-4.05670.30861300.23772717X-RAY DIFFRACTION100
4.0567-4.31070.28151370.22142716X-RAY DIFFRACTION100
4.3107-4.64330.28961450.19522747X-RAY DIFFRACTION100
4.6433-5.110.2691540.19572708X-RAY DIFFRACTION100
5.11-5.84830.29871440.21662730X-RAY DIFFRACTION100
5.8483-7.36350.29281400.22162755X-RAY DIFFRACTION100
7.3635-46.60810.2151460.18532809X-RAY DIFFRACTION99

+
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