[English] 日本語
Yorodumi
- PDB-1tx0: Dihydropteroate Synthetase, With Bound Product Analogue Pteroic A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tx0
TitleDihydropteroate Synthetase, With Bound Product Analogue Pteroic Acid, From Bacillus anthracis
ComponentsDHPS, Dihydropteroate synthase
KeywordsTRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
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
PTEROIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBabaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal Structure of 7,8-Dihydropteroate Synthase from Bacillus anthracis; Mechanism and Novel Inhibitor Design.
Authors: Babaoglu, K. / Qi, J. / Lee, R.E. / White, S.W.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water2,954164
1
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
2
B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,35314
Polymers65,7672
Non-polymers1,58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)97.547, 97.547, 263.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYAA2 - 2422 - 44
21LYSLYSGLYGLYBB2 - 2422 - 44
32SERSERGLYGLYAA38 - 6358 - 83
42SERSERGLYGLYBB38 - 6358 - 83
53SERSERLYSLYSAA75 - 27495 - 294
63SERSERLYSLYSBB75 - 27495 - 294
DetailsThe biological dimer is generated by the two fold axis: x,y,z

-
Components

#1: Protein DHPS, Dihydropteroate synthase /


Mass: 32883.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: str. A2012 / Gene: folp / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q81VW8, dihydropteroate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: lithium sulfate, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2004 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→81.7 Å / Num. all: 38829 / Num. obs: 38829 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.066 / Net I/σ(I): 18.3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 38829 / Rsym value: 0.577 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TWS

1tws


Resolution: 2.15→81.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.422 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 0.243 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27963 1954 5 %RANDOM
Rwork0.23057 ---
all0.23298 36872 --
obs0.23298 36872 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.459 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å22.25 Å20 Å2
2--4.49 Å20 Å2
3----6.74 Å2
Refinement stepCycle: LAST / Resolution: 2.15→81.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 96 164 4338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224228
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9925707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335521
X-RAY DIFFRACTIONr_chiral_restr0.110.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023111
X-RAY DIFFRACTIONr_nbd_refined0.2260.22051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.25
X-RAY DIFFRACTIONr_mcbond_it0.8751.52605
X-RAY DIFFRACTIONr_mcangle_it1.65824189
X-RAY DIFFRACTIONr_scbond_it2.83631623
X-RAY DIFFRACTIONr_scangle_it4.2424.51518
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
996tight positional0.060.05
949medium positional0.430.5
996tight thermal0.230.5
949medium thermal0.982
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.402 134
Rwork0.367 2670
obs-2894
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)
10.57950.08680.27910.7391-0.11651.6251-0.1249-0.06110.02510.0385-0.0015-0.01290.10620.35260.12640.21590.21580.00830.22730.05830.2151-78.29579.961491.349
20.2142-0.0607-0.07820.6342-0.05621.0691-0.00480.0686-0.0408-0.1323-0.1393-0.0252-0.32710.11940.14410.26710.0686-0.03730.26780.06790.1783-67.723160.9851138.5923
3-0.08190.07470.13430.0565-0.33380.49030.0118-0.03830.0261-0.0228-0.069-0.04-0.09920.05440.05720.28910.18480.00120.20790.05620.302-76.179970.5575112.9455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274
3X-RAY DIFFRACTION3A284 - 371
4X-RAY DIFFRACTION3B284 - 359
5X-RAY DIFFRACTION3A278

+
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