[English] 日本語
Yorodumi
- PDB-1e3z: Acarbose complex of chimaeric amylase from B. amyloliquefaciens a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e3z
TitleAcarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / AMYLASE / FAMILY 13 / ACARBOSE / COMPLEX
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-ACI / Alpha-amylase / Alpha-amylase
Similarity search - Component
Biological speciesBACILLUS AMYLOLIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBrzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J.
CitationJournal: Biochemistry / Year: 2000
Title: Structural Analysis of a Chimeric Bacterial Alpha-Amylase. High Resolution Analysis of Native and Ligand Complexes
Authors: Brzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J.
History
DepositionJun 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84012
Polymers55,0381
Non-polymers1,80211
Water12,250680
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.720, 78.270, 238.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ALPHA-AMYLASE


Mass: 55038.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHIMAERIC STRUCTURE CONSISTING OF RESIDUES 1 - 300 OF B. AMYLOLIQUEFACIENS AND RESIDUES 301 - 483 OF B. LICHENIFORMIS IN COMPLEX WITH ACARBOSE
Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Description: SYNTHETIC GENE / Production host: BACILLUS AMYLOLIQUEFACIENS (bacteria) / References: UniProt: P00692, UniProt: P06278, alpha-amylase

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 310.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a21d2m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 472.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a21d2m-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 688 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACI / 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL


Mass: 175.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H13NO4 / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE PSEUDODECASACCHARIDE IN THIS STRUCTURE IS RELATED TO THE POLYSACHARIDE ACARBOSE: O-4,6-DIDEOXY- ...THE PSEUDODECASACCHARIDE IN THIS STRUCTURE IS RELATED TO THE POLYSACHARIDE ACARBOSE: O-4,6-DIDEOXY-4-[[[1S-(1.ALPHA.,4.ALPHA.,5.BETA.,6.ALPHA.)]- 4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)-2-CYCLOHEXEN-1-YL]AMINO]- .ALPHA.-D-GLUCOPYRANOSYL-(1->4)-O-.ALPHA.-D-GLUCOPYRANOSYL- (1->4)-D-GLUCOSE ACARBOSE IS A PSEUDOTETRASACCHARIDE CONTAINING AN UNSATURATED CYCLITOL MOIETY. AN .ALPHA.-GLUCOSIDASE INHIBITOR THAT REDUCES SUGAR ABSORPTION IN THE GASTROINTESTINAL TRACT. FOR MORE INFORMATION ABOUT ACARBOSE PLEASE SEE: REVIEW OF PHARMACODYNAMICS, PHARMACOKINETICS AND THERAPEUTIC POTENTIAL: S. P. CLISSOLD, C. EDWARDS, DRUGS 35, 214-243 (1988). THERAP CAT: ANTIDIABETIC.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING ...Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM ACARBOSE SOLUTION TO OBTAIN THE COMPLEX.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18-13 %(w/v)mmePEG20001reservoiror PEG5000
20.1 MTris-HCl1drop
35 mM1dropCaCl2
430-35 Mprotein1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 38273 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 10 / % possible all: 99
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 10

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3X

1e3x


Resolution: 1.93→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1844 5 %RANDOM
Rwork0.13 ---
obs-36166 100 %-
Displacement parametersBiso mean: 12.1 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 113 680 4693
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2232
X-RAY DIFFRACTIONp_mcangle_it1.7913
X-RAY DIFFRACTIONp_scbond_it1.6972
X-RAY DIFFRACTIONp_scangle_it2.6553
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1180.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.1950.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.13 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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