[English] 日本語
Yorodumi
- PDB-1h49: CRYSTAL STRUCTURE OF THE INACTIVE DOUBLE MUTANT OF THE MAIZE BETA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h49
TitleCRYSTAL STRUCTURE OF THE INACTIVE DOUBLE MUTANT OF THE MAIZE BETA-GLUCOSIDASE ZMGLU1-E191D-F198V IN COMPLEX WITH DIMBOA-GLUCOSIDE
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / INACTIVE MUTANT E191D
Function / homology
Function and homology information


galactosidase activity / fucosidase activity / xylanase activity / DIMBOA glucoside beta-D-glucosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / beta-glucosidase / beta-glucosidase activity ...galactosidase activity / fucosidase activity / xylanase activity / DIMBOA glucoside beta-D-glucosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / beta-glucosidase / beta-glucosidase activity / chloroplast / carbohydrate metabolic process
Similarity search - Function
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-D-glucopyranose / Chem-HBO / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic
Similarity search - Component
Biological speciesZEA MAYS (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCzjzek, M. / Moriniere, J. / Verdoucq, L. / Bevan, D.R. / Henrissat, B. / Esen, A.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Mutational and Structural Analysis of Aglycone Specificity in Maize and Sorghum Beta-Glucosidases
Authors: Verdoucq, L. / Czjzek, M. / Moriniere, J. / Bevan, D.R. / Esen, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Mechanism of Substrate (Aglycone) Specificity in Beta-Glucosidases is Revealed by Crystal Structures of Mutant Maize Beta-Glucosidase -Dimboa, -Dimboaglc, and -Dhurrin Complexes
Authors: Czjzek, M. / Cicek, M. / Zamboni, V. / Bevan, D.R. / Henrissat, B. / Esen, A.
History
DepositionFeb 25, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-GLUCOSIDASE
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6036
Polymers116,8212
Non-polymers7834
Water8,845491
1
A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8023
Polymers58,4101
Non-polymers3912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8023
Polymers58,4101
Non-polymers3912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.145, 114.088, 80.126
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 29
2116B1 - 29
1212A30 - 36
2212B30 - 36
1315A37 - 50
2315B37 - 50
1412A50 - 60
2412B50 - 60
1515A60 - 184
2515B60 - 184
1612A184 - 200
2612B184 - 200
1715A201 - 225
2715B201 - 225
1812A226 - 238
2812B226 - 238
1915A239 - 253
2915B239 - 253
11012A254 - 265
21012B254 - 265
11115A266 - 272
21115B266 - 272
11212A273 - 291
21212B273 - 291
11315A292 - 327
21315B292 - 327
11412A328 - 342
21412B328 - 342
11515A343 - 401
21515B343 - 401
11612A402 - 410
21612B402 - 410
11715A411 - 449
21715B411 - 449
11812A450 - 476
21812B450 - 476
11915A477 - 490
21915B477 - 490
12016A490 - 501
22016B490 - 501

NCS oper: (Code: given
Matrix: (-0.97409, -0.17051, 0.14857), (-0.17723, 0.16748, -0.96981), (0.14048, -0.97102, -0.19337)
Vector: 24.74996, 141.19318, 165.7684)

-
Components

#1: Protein BETA-GLUCOSIDASE / CHLOROPLAST PRECURSOR / GENTIOBIASE / CELLOBIASE / BETA-D-GLUCOSIDE GLUCOHYDROLASE / GLU1


Mass: 58410.383 Da / Num. of mol.: 2 / Fragment: BETA-GLUCOSIDASE, RESIDUES 55-566 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: IN COMPLEX WITH THE LIGAND DIMBOA-GLUCOSIDE / Source: (gene. exp.) ZEA MAYS (maize) / Strain: CV. MUTIN / Tissue: COLEOPTILE / Cell: PLYS S CELLS / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49235, beta-glucosidase
#2: Chemical ChemComp-HBO / 2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE


Mass: 211.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO5
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATIONS GLU 245 ASP AND PHE 252 VAL, CHAINS A,B
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5 22 % PEG 4000, 5 % ISOPROPANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorDate: Nov 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67417 / % possible obs: 86.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.5 / % possible all: 52

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4L

1e4l


Resolution: 1.9→79.06 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.361 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3519 5 %RANDOM
Rwork0.184 ---
obs0.185 67417 86.5 %-
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: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å2-2.7 Å2
2---2.11 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 52 491 8469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0218224
X-RAY DIFFRACTIONr_bond_other_d0.0050.027006
X-RAY DIFFRACTIONr_angle_refined_deg1.431.94811174
X-RAY DIFFRACTIONr_angle_other_deg0.974316378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215978
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_restr0.0960.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029244
X-RAY DIFFRACTIONr_gen_planes_other0.010.021762
X-RAY DIFFRACTIONr_nbd_refined0.2520.22078
X-RAY DIFFRACTIONr_nbd_other0.2450.28554
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.24255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.54880
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09127862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.70133344
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6914.53312
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1986tight positional0.130.05
5062medium positional0.240.5
509loose positional0.345
1986tight thermal0.130.5
5062medium thermal0.512
509loose thermal1.110
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.281 317
Rwork0.256 6120
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)
10.8160.86050.27771.20340.5950.46960.1738-0.0336-0.13330.2707-0.0553-0.22710.09490.0403-0.11840.1472-0.0281-0.02180.1444-0.00630.132117.895114.24479.935
20.53180.19580.31430.92250.52830.6502-0.00470.1002-0.0149-0.0980.0499-0.0874-0.10240.0527-0.04530.04710.00070.0650.1503-0.02930.0958-0.60379.99941.709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 501
2X-RAY DIFFRACTION2B1 - 501

+
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