[English] 日本語
Yorodumi
- PDB-5hqb: A Glycoside Hydrolase Family 97 enzyme (E480Q) in complex with Pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hqb
TitleA Glycoside Hydrolase Family 97 enzyme (E480Q) in complex with Panose from Pseudoalteromonas sp. strain K8
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / glucoside hydrolase / Family 97 / chloride
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Glycoside hydrolase-type carbohydrate-binding / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily ...Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Glycoside hydrolase-type carbohydrate-binding / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Alpha-glucosidase
Similarity search - Component
Biological speciesPseudoalteromonas sp. K8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, J. / He, C. / Xiao, Y.
CitationJournal: J. Struct. Biol. / Year: 2016
Title: Structures of PspAG97A alpha-glucoside hydrolase reveal a novel mechanism for chloride induced activation.
Authors: He, C. / Li, J. / Li, W. / Xue, Y. / Fang, Z. / Fang, W. / Zhang, X. / Wang, X. / Xiao, Y.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...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 / 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-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,81314
Polymers75,5741
Non-polymers1,23813
Water16,448913
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.167, 119.167, 181.832
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-988-

HOH

21A-1705-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alpha-glucosidase /


Mass: 75574.344 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-680 / Mutation: E480Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. K8 (bacteria) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Y0DFX2
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 925 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 4.93 Å3/Da / Density % sol: 75.06 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris-HCl (pH 6.5), 0.1M magnesium formate dihydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 137668 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 19.26 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Χ2: 0.699 / Net I/av σ(I): 15.067 / Net I/σ(I): 4.3 / Num. measured all: 838357
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.865.90.594135800.8190.2610.650.51799
1.86-1.946.30.479135560.8850.2040.5210.58899.3
1.94-2.036.20.326136390.9420.140.3550.55199.5
2.03-2.1360.249137050.9610.1090.2730.60399.6
2.13-2.275.90.194136360.9710.0860.2130.69999.4
2.27-2.446.30.151137500.9850.0640.1640.63599.8
2.44-2.696.20.12137770.9890.0520.1310.67799.8
2.69-3.0860.091138080.9920.040.0990.75499.7
3.08-3.886.20.073139830.9950.0320.080.944100
3.88-405.90.065142340.9950.0290.0721.01799.2

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HQ4

5hq4


Resolution: 1.8→39.291 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1553 6906 5.02 %
Rwork0.1365 130669 -
obs0.1374 137575 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 24.1053 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 1.8→39.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5278 0 77 913 6268
Biso mean--38.89 38.77 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075567
X-RAY DIFFRACTIONf_angle_d0.8537574
X-RAY DIFFRACTIONf_chiral_restr0.058804
X-RAY DIFFRACTIONf_plane_restr0.005981
X-RAY DIFFRACTIONf_dihedral_angle_d13.0813243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8005-1.82090.26122220.24144258448098
1.8209-1.84230.23722360.21694303453999
1.8423-1.86480.21442180.19514327454599
1.8648-1.88840.20292270.18434287451499
1.8884-1.91330.2222280.18494288451699
1.9133-1.93950.20652020.181643404542100
1.9395-1.96720.16652180.150943384556100
1.9672-1.99650.15372360.14734317455399
1.9965-2.02770.1492310.147743014532100
2.0277-2.0610.16452080.145343554563100
2.061-2.09650.17332390.152743084547100
2.0965-2.13460.1642270.145543484575100
2.1346-2.17570.16362210.14284334455599
2.1757-2.22010.15672360.1354318455499
2.2201-2.26840.16071990.144443414540100
2.2684-2.32110.1422370.135343554592100
2.3211-2.37920.16442450.136543404585100
2.3792-2.44350.16692260.13943434569100
2.4435-2.51540.16292250.13943504575100
2.5154-2.59650.16722290.13543744603100
2.5965-2.68930.14542390.132243654604100
2.6893-2.7970.15092540.130743554609100
2.797-2.92420.13872310.12754350458199
2.9242-3.07830.15172290.125843784607100
3.0783-3.27110.15412560.12543914647100
3.2711-3.52350.13122460.118644044650100
3.5235-3.87780.14962210.118344474668100
3.8778-4.43830.14022410.10814396463799
4.4383-5.58920.11812350.114944704705100
5.5892-39.29990.16082440.16024588483298
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)
10.5620.23740.03250.79520.14520.6828-0.09440.0445-0.0732-0.04640.04330.03370.1083-0.11920.04460.168-0.05220.01520.1072-0.0080.144342.7436-12.540914.7021
21.22410.50070.45561.28450.39782.289-0.11260.1999-0.09-0.32460.1088-0.2016-0.01350.11480.00310.2527-0.07580.0660.1302-0.01080.176167.65543.4343-6.5721
30.84830.039-0.25390.4948-0.06130.6614-0.04960.13590.1425-0.12070.07060.0266-0.1341-0.0995-0.02380.2146-0.0325-0.0340.10770.02550.152146.94715.98634.6615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 20 through 276)A20 - 276
2X-RAY DIFFRACTION2(chain 'A' and resid 586 through 681)A586 - 681
3X-RAY DIFFRACTION3(chain 'A' and resid 277 through 585)A277 - 585

+
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