[English] 日本語
Yorodumi
- PDB-3h2e: Structural Studies of Pterin-Based Inhibitors of Dihydropteroate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h2e
TitleStructural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase
ComponentsDihydropteroate synthase
KeywordsTransferase/Transferase Inhibitor / ANTHRACIS / FOLATE BIOSYNTHESIS / DIHYDROPTEROATE / PTERINE / Transferase / Transferase-Transferase Inhibitor COMPLEX
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 / 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 ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / 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
Chem-B59 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis str. A2012 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYun, M.-K. / White, S.W.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structural studies of pterin-based inhibitors of dihydropteroate synthase.
Authors: Hevener, K.E. / Yun, M.K. / Qi, J. / Kerr, I.D. / Babaoglu, K. / Hurdle, J.G. / Balakrishna, K. / White, S.W. / Lee, R.E.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,00812
Polymers65,7672
Non-polymers1,24110
Water4,612256
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,53610
Polymers65,7672
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area3750 Å2
ΔGint-108 kcal/mol
Surface area22030 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,48114
Polymers65,7672
Non-polymers1,71312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Buried area3670 Å2
ΔGint-95 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.063, 98.063, 263.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Dihydropteroate synthase


Mass: 32883.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. A2012 (bacteria)
Gene: folP, BAO_0074 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1UXN2, UniProt: Q81VW8*PLUS, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-B59 / 1,3-dimethyl-2,4,7-trioxo-1,2,3,4,7,8-hexahydropteridine-6-carbaldehyde


Mass: 236.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: LITHIUM SULFATE, propane, Bis-Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.21 Å / Num. obs: 48615 / % possible obs: 94.2 % / Redundancy: 11.5 % / Rsym value: 0.102 / Net I/σ(I): 32.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.346 / % possible all: 60.8

-
Processing

Software
NameVersionClassification
SERGUIControldata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TX0

1tx0


Resolution: 2→48.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.966 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23735 2447 5 %RANDOM
Rwork0.20176 ---
obs0.20361 48547 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.345 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.72 Å20 Å2
2--1.43 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 73 256 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.995765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2225.08187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78515785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8071525
X-RAY DIFFRACTIONr_chiral_restr0.0960.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21780
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22915
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0071.52743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48224255
X-RAY DIFFRACTIONr_scbond_it2.3431810
X-RAY DIFFRACTIONr_scangle_it3.7864.51508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 101 -
Rwork0.224 2050 -
obs--58.14 %
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)
11.38-0.07020.53030.89620.08712.0022-0.02880.0071-0.00250.06450.03220.02770.02360.1465-0.0035-0.07820.11370.0103-0.03350.0289-0.2085-78.43980.83491.339
20.79230.0247-0.24461.1985-0.25251.5735-0.00890.0538-0.0109-0.1512-0.0733-0.0245-0.23670.09080.08220.0559-0.0151-0.0453-0.10460.0352-0.1959-68.26761.351138.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274

+
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