[English] 日本語
Yorodumi
- PDB-1gxs: Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gxs
TitleCrystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme
Components(P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN ...) x 2
KeywordsLYASE / INHIBITOR COMPLEX / CYANOGENESIS MECHANISM
Function / homology
Function and homology information


hydroxymandelonitrile lyase / hydroxymandelonitrile lyase activity
Similarity search - Function
Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain ...Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / DECANOIC ACID / P-(S)-hydroxymandelonitrile lyase / P-(S)-hydroxymandelonitrile lyase
Similarity search - Component
Biological speciesSORGHUM BICOLOR (sorghum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal Structure of Hydroxynitrile Lyase from Sorghum Bicolor in Complex with the Inhibitor Benzoic Acid: A Novel Cyanogenic Enzyme
Authors: Lauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F.
History
DepositionApr 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A
B: P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B
C: P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A
D: P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,39012
Polymers96,2174
Non-polymers2,1728
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26280 Å2
ΔGint-78.9 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.700, 103.700, 90.600
Angle α, β, γ (deg.)90.00, 101.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE BIOLOGICALLY ACTIVE SUBUNIT IS A HETEROTETRAMER FORMED BY TWO AB-HETERODIMERS

-
Components

-
P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN ... , 2 types, 4 molecules ACBD

#1: Protein P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A / HNL / HYDROXYNITRILE LYASE


Mass: 30395.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOENZYME II / Source: (natural) SORGHUM BICOLOR (sorghum) / Tissue: PRIMARY LEAVES OF SEEDLINGS
References: UniProt: Q8W4X3, UniProt: P52708*PLUS, hydroxymandelonitrile lyase
#2: Protein P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B / HNL / HYDROXYNITRILE LYASE


Mass: 17713.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOENZYME II / Source: (natural) SORGHUM BICOLOR (sorghum) / Tissue: PRIMARY LEAVES OF SEEDLINGS
References: UniProt: Q8W4X3, UniProt: P52708*PLUS, hydroxymandelonitrile lyase

-
Sugars , 2 types, 4 molecules

#3: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 335 molecules

#4: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsVARIANTS LISTED IN SEQADV RECORDS WERE SUPPLIED BY THE AUTHORS OF THE PDB ENTRY, AND WERE NOT ...VARIANTS LISTED IN SEQADV RECORDS WERE SUPPLIED BY THE AUTHORS OF THE PDB ENTRY, AND WERE NOT OBTAINED FROM THE SWISS-PROT ENTRY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61 %
Crystal growpH: 5.4
Details: 100MM NA-CITRATE PH 5.4 USING 1.6 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Lauble, H., (1996) Acta Crystallogr., D52, 887.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
2100 mMbenzoic acid1drop
3100 mMsodium citrate1droppH5.4
41.6 Mammonium sulfate1reservoir
5100 mMsodium citrate1reservoirpH5.4

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→17 Å / Num. obs: 100992 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 15.6 Å2 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.7 / % possible all: 82.9
Reflection
*PLUS
Lowest resolution: 17 Å / Num. obs: 51747 / Num. measured all: 100992 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 82.9 % / Rmerge(I) obs: 0.114

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SC2

3sc2


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: ASYMMETRIC UNIT CONTAINS 2 ALPHA/ BETA-DIMERS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5122 10.1 %RANDOM
Rwork0.165 ---
obs0.165 50480 85.2 %-
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 146 331 7225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.611.5
X-RAY DIFFRACTIONx_mcangle_it3.912
X-RAY DIFFRACTIONx_scbond_it4.422
X-RAY DIFFRACTIONx_scangle_it6.322.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 655 10.3 %
Rwork0.216 5693 -
obs--64.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19XHOH.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARBEZ.PROTOPBEZ.PRO
X-RAY DIFFRACTION3PARDKA.PROTOPDKA.PRO
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

+
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