[English] 日本語
Yorodumi
- PDB-4gxp: Chimeric Family 1 beta-glucosidase made with non-contiguous SCHEMA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gxp
TitleChimeric Family 1 beta-glucosidase made with non-contiguous SCHEMA
ComponentsBeta-glucosidase Chimeric protein
KeywordsHYDROLASE / chimeragenesis / protein recombination / eukaryotic-prokaryotic chimera / GH1 / beta-glucosidase
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-glucosidase / Beta-glucosidase A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Trichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSmith, M.A. / Romero, P.A. / Wu, T. / Brustad, E.M. / Arnold, F.H.
CitationJournal: Protein Sci. / Year: 2013
Title: Chimeragenesis of distantly-related proteins by noncontiguous recombination.
Authors: Smith, M.A. / Romero, P.A. / Wu, T. / Brustad, E.M. / Arnold, F.H.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-glucosidase Chimeric protein
B: Beta-glucosidase Chimeric protein
C: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)159,0793
Polymers159,0793
Non-polymers00
Water362
1
A: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.377, 115.377, 282.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Beta-glucosidase Chimeric protein / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 53026.301 Da / Num. of mol.: 3
Fragment: UNP Q08638 residues 1-160,204-217,352-380,395-446 and UNP O93785 residues 160-302,221-367,399-413
Mutation: Y120F,W134L,A135L,H378Y,Q336A,S337M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria), (gene. exp.) Trichoderma reesei (fungus)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: bglA, bgl2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08638, UniProt: O93785, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% polyethylene glycol 3350, 0.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012
RadiationMonochromator: Liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→37.43 Å / Num. all: 43376 / Num. obs: 43376 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.052 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3-3.164.80.38120.381199.6
3.16-3.355.30.2423.10.242199.8
3.35-3.5950.1435.10.143199.8
3.59-3.875.10.097.80.09199.8
3.87-4.2450.0689.30.068199.8
4.24-4.744.70.05111.80.051199.8
4.74-5.484.90.04414.20.044199.5
5.48-6.714.80.03716.70.037199.7
6.71-9.494.70.0319.20.03199.3
9.49-37.4294.60.02523.10.025197.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XSCALEdata scaling
MOLREP(CCP4 6.2)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 59.565 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R: 1.788 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29377 2188 5.1 %RANDOM
Rwork0.2389 ---
obs0.24164 41124 99.47 %-
all-43315 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 3→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9867 0 0 2 9869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.90813956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70851360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35223.124461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.927151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0291555
X-RAY DIFFRACTIONr_chiral_restr0.1240.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 165 -
Rwork0.324 2841 -
obs--99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1616-0.14340.40360.65950.06842.247-0.1284-0.2135-0.2314-0.29650.29220.0707-0.5830.0078-0.16381.0373-0.19240.01571.67350.06671.22912.408213.14721.653
21.52170.50580.41150.2503-0.05441.11510.0939-0.0877-0.3299-0.030.03790.0836-0.020.3401-0.13170.53530.1706-0.10122.1206-0.05151.292923.4516-16.507337.1928
31.770.1145-0.45930.4556-0.56871.52250.18581.2683-0.08640.2211-0.49170.2006-0.21360.89980.30590.2353-0.0802-0.053.4640.3040.866362.05360.177916.4891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 466
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B11 - 466
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C11 - 467

+
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