[English] 日本語
Yorodumi
- PDB-1twz: Dihydropteroate Synthetase, With Bound Substrate Analogue PtP, Fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1twz
TitleDihydropteroate Synthetase, With Bound Substrate Analogue PtP, 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
PTERIN-6-YL-METHYL-MONOPHOSPHATE / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBabaoglu, K. / Qi, J. / Lee, R.L. / 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 / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 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.beg_label_asym_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)67,08212
Polymers65,7672
Non-polymers1,31510
Water2,414134
1
A: DHPS, Dihydropteroate synthase
hetero molecules

A: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,08212
Polymers65,7672
Non-polymers1,31510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area4670 Å2
ΔGint-96 kcal/mol
Surface area21880 Å2
MethodPISA, PQS
2
B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5416
Polymers32,8841
Non-polymers6575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DHPS, Dihydropteroate synthase
hetero molecules

B: DHPS, Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,08212
Polymers65,7672
Non-polymers1,31510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465-x-1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.362, 97.362, 262.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-327-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
12A
22A

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSASNASNAA2 - 2722 - 47
211LYSLYSASNASNBB2 - 2722 - 47
321TYRTYRILEILEAA39 - 6259 - 82
421TYRTYRILEILEBB39 - 6259 - 82
531GLUGLULYSLYSAA78 - 27498 - 294
631GLUGLULYSLYSBB78 - 27498 - 294
112PMMPMMPMMPMMA - BG - L282
212PMMPMMPMMPMMA - BG - L282

NCS ensembles :
ID
1
2
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.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE


Mass: 273.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N5O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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 219K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 13, 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: 2.75→50 Å / Num. all: 19781 / Num. obs: 19781 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rsym value: 0.057 / Net I/σ(I): 57.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 12 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 19781 / Rsym value: 0.324 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TWS

1tws


Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.324 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / ESU R: 1.079 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27848 1004 5.1 %RANDOM
Rwork0.22601 ---
all0.22871 18715 --
obs0.22871 18715 98.3 %-
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: 30.082 Å2
Baniso -1Baniso -2Baniso -3
1-4.38 Å22.19 Å20 Å2
2--4.38 Å20 Å2
3----6.56 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 76 134 4303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224223
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9875702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965523
X-RAY DIFFRACTIONr_chiral_restr0.1060.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023103
X-RAY DIFFRACTIONr_nbd_refined0.2560.22231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4260.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.25
X-RAY DIFFRACTIONr_mcbond_it0.6031.52615
X-RAY DIFFRACTIONr_mcangle_it1.17824205
X-RAY DIFFRACTIONr_scbond_it1.81331608
X-RAY DIFFRACTIONr_scangle_it2.8984.51497
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1937tight positional0.120.05
22B36tight positional00.05
11A1937tight thermal0.110.5
22B36tight thermal00.5
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.38 85
Rwork0.305 1344
obs-1429
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)
12.1238-0.08430.01711.9349-0.04474.1946-0.1919-0.19960.02580.2062-0.022-0.28170.25110.83940.2140.210.2275-0.01590.28610.08350.2806-78.174179.871391.3175
21.71540.09730.25011.8141-0.06323.918-0.10890.25510.2142-0.3165-0.1661-0.0927-0.85160.24260.27490.46820.0533-0.06350.17740.10240.266-67.439760.8303138.4964
3-0.23780.3339-0.0519-0.72680.33190.57090.13010.02230.0133-0.0415-0.1563-0.03370.05470.04760.02620.28660.1540.01530.19310.07990.1524-75.221969.1002113.4019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 274
3X-RAY DIFFRACTION3A283 - 289
4X-RAY DIFFRACTION3B283 - 288
5X-RAY DIFFRACTION3A278 - 281
6X-RAY DIFFRACTION3B278 - 281

+
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