[English] 日本語
Yorodumi
- PDB-4db7: Crystal structure of B. anthracis DHPS with compound 25 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4db7
TitleCrystal structure of B. anthracis DHPS with compound 25
ComponentsDihydropteroate Synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / Transferase / pABA / DHPP / 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-Z25 / : / Dihydropteroate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHammoudeh, D. / Lee, R.E. / White, S.W.
CitationJournal: Chemmedchem / Year: 2012
Title: Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity.
Authors: Zhao, Y. / Hammoudeh, D. / Yun, M.K. / Qi, J. / White, S.W. / Lee, R.E.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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_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: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,13413
Polymers65,7672
Non-polymers1,36711
Water66737
1
A: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,03812
Polymers65,7672
Non-polymers1,27110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3760 Å2
ΔGint-99 kcal/mol
Surface area21510 Å2
MethodPISA
2
B: Dihydropteroate Synthase
hetero molecules

B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,23014
Polymers65,7672
Non-polymers1,46312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area4020 Å2
ΔGint-122 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.695, 99.695, 263.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 (anthrax bacterium) / Strain: A2012 / Gene: folP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3P9L8, UniProt: Q81VW8*PLUS, dihydropteroate synthase
#2: Chemical ChemComp-Z25 / 3-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)propanoic acid


Mass: 251.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9N5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Lithium sulfate, Bis-Tris propane, pH 9.0, 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 300 mm CCD / Detector: CCD / Date: Nov 13, 2011
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 23895 / Num. obs: 23895 / % possible obs: 86.4 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.057 / Χ2: 1.129 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.596.80.1668.94711951.2444.9
2.59-2.696.90.1697.93815521.24957.4
2.69-2.827.10.1579.21420271.24375
2.82-2.968.30.15711.53225231.17393
2.96-3.1510.10.13118.45527041.13299.9
3.15-3.3910.70.08927.34927421.14899.9
3.39-3.7310.60.06536.20727121.2199.1
3.73-4.2710.50.05130.41727690.99399.3
4.27-5.3810.30.04334.72928241.06399.5
5.38-308.90.04328.45628471.06693.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TWS

1tws


Resolution: 2.5→28.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2969 / WRfactor Rwork: 0.2512 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7102 / SU B: 26.547 / SU ML: 0.254 / SU R Cruickshank DPI: 0.5117 / SU Rfree: 0.3088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 1215 5.1 %RANDOM
Rwork0.2315 ---
obs0.2333 23738 85.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 153.15 Å2 / Biso mean: 76.9998 Å2 / Biso min: 44.16 Å2
Baniso -1Baniso -2Baniso -3
1-5.7 Å22.85 Å2-0 Å2
2--5.7 Å2-0 Å2
3----8.54 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3999 0 81 37 4117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224130
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9935571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0615508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79325.163184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59115764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9971524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213037
X-RAY DIFFRACTIONr_mcbond_it0.911.52544
X-RAY DIFFRACTIONr_mcangle_it1.7524086
X-RAY DIFFRACTIONr_scbond_it2.11731586
X-RAY DIFFRACTIONr_scangle_it3.6714.51485
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 41 -
Rwork0.347 791 -
all-832 -
obs--42.36 %
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)
10.5208-0.02180.23241.1216-0.02241.27490.0045-0.18820.07280.0303-0.0528-0.01470.267-0.03440.04820.2512-0.09380.03640.36330.07970.0786-19.281624.31183.6198
21.17440.290.05940.5652-0.031.5173-0.01610.17470.0224-0.0081-0.05250.1055-0.01390.3190.06860.2551-0.09230.01790.2880.0870.0899-30.9584.863851.4997
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