[English] 日本語
Yorodumi
- PDB-1eye: 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eye
Title1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTEROATE SYNTHASE (DHPS) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 6-HYDROXYMETHYLPTERIN MONOPHOSPHATE
ComponentsDIHYDROPTEROATE SYNTHASE I
KeywordsTRANSFERASE / alpha-beta barrel
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PTERIN-6-YL-METHYL-MONOPHOSPHATE / Dihydropteroate synthase / Dihydropteroate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBaca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of Mycobacterium tuberculosis 7,8-dihydropteroate synthase in complex with pterin monophosphate: new insight into the enzymatic mechanism and sulfa-drug action.
Authors: Baca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROPTEROATE SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1703
Polymers28,8731
Non-polymers2972
Water4,396244
1
A: DIHYDROPTEROATE SYNTHASE I
hetero molecules

A: DIHYDROPTEROATE SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3416
Polymers57,7462
Non-polymers5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4280 Å2
ΔGint-53 kcal/mol
Surface area20350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.900, 62.900, 121.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

-
Components

#1: Protein DIHYDROPTEROATE SYNTHASE I / / DHPS 1


Mass: 28872.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PKOS007-90 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A578, UniProt: P9WND1*PLUS, dihydropteroate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Details: PtP was synthesized from 6-hydroxymethyl pterin and pyrophosphoric acid as described by Shiota et al., 1964
#3: Chemical ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE


Mass: 273.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N5O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, Sodium Acetate, Ammonium Acetate, para-aminosalicylic acid, 6-hydroxymethl pterin monophosphate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
2200 mMammonium acetate1reservoir
330 %(w/v)PEG40001reservoir
43 mMPtP1reservoir
53 mMpABA1reservoir

-
Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26.5 Å / Num. all: 136341 / Num. obs: 25211 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 20.649 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.411
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.177 / Num. unique all: 2137 / % possible all: 69.9
Reflection
*PLUS
Num. measured all: 136341
Reflection shell
*PLUS
% possible obs: 69.9 %

-
Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT default
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1236 -RANDOM
Rwork0.185 ---
all0.185 25211 --
obs0.185 25211 80.5 %-
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 19 244 2110
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.6
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

+
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