[English] 日本語
Yorodumi
- PDB-8sv5: Crystal structure of Bacillus anthracis dihydroneopterin aldolase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sv5
TitleCrystal structure of Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
Components7,8-dihydroneopterin aldolase
KeywordsLYASE / dihydroneopterin aldolase / DHNA / 6-hydroxymethyl-7 / 8-dihydropterin / product / product complex
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
Chem-PH2 / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsShaw, G.X. / Li, Y. / Yan, H. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
Authors: Shaw, G.X. / Li, Y. / Yan, H. / Ji, X.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
E: 7,8-dihydroneopterin aldolase
F: 7,8-dihydroneopterin aldolase
G: 7,8-dihydroneopterin aldolase
H: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64518
Polymers111,9598
Non-polymers1,68610
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26780 Å2
ΔGint-65 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.421, 101.849, 77.204
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
7,8-dihydroneopterin aldolase


Mass: 13994.912 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: folB, GBAA_0072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L7HSV1, dihydroneopterin aldolase
#2: Chemical
ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H9N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium acetate, cacodylate, etc.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2006 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 49567 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.065 / Rrim(I) all: 0.133 / Χ2: 0.953 / Net I/σ(I): 7.7 / Num. measured all: 173082
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.231.70.74240090.4680.7980.6240.9750.9478.7
2.23-2.3220.65345850.5690.8510.5160.8370.97489.1
2.32-2.422.50.63549520.6450.8860.4540.7850.9796.2
2.42-2.553.20.5750890.7190.9140.3670.680.9799.5
2.55-2.713.90.46351440.8430.9560.2670.5360.957100
2.71-2.924.20.33751150.9190.9790.1860.3850.944100
2.92-3.214.30.21551270.9640.9910.1170.2450.95699.9
3.21-3.674.20.1251500.9840.9960.0660.1370.96599.7
3.67-4.634.20.0751620.9930.9980.0390.080.9899.8
4.63-304.20.07152340.9940.9980.0380.0810.89699.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8SU7

8su7


Resolution: 2.16→29.88 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1999 4.04 %Random selection
Rwork0.1807 ---
obs0.1826 49504 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 120 183 8167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038150
X-RAY DIFFRACTIONf_angle_d0.63111004
X-RAY DIFFRACTIONf_dihedral_angle_d18.573146
X-RAY DIFFRACTIONf_chiral_restr0.061184
X-RAY DIFFRACTIONf_plane_restr0.0061416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.37121070.30632549X-RAY DIFFRACTION72
2.21-2.270.33511260.28012978X-RAY DIFFRACTION84
2.27-2.340.36591350.27013225X-RAY DIFFRACTION92
2.34-2.420.33551430.24813382X-RAY DIFFRACTION96
2.42-2.50.27361470.24053501X-RAY DIFFRACTION99
2.5-2.60.27381480.21533514X-RAY DIFFRACTION100
2.6-2.720.27011490.19993543X-RAY DIFFRACTION100
2.72-2.860.26061480.18663511X-RAY DIFFRACTION100
2.86-3.040.21841490.19113536X-RAY DIFFRACTION100
3.04-3.280.25061480.18423522X-RAY DIFFRACTION100
3.28-3.610.22751490.16753537X-RAY DIFFRACTION100
3.61-4.130.19741480.15353546X-RAY DIFFRACTION100
4.13-5.20.17411500.14193557X-RAY DIFFRACTION100
5.2-29.880.19261520.1743604X-RAY DIFFRACTION100

+
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://pdbjlvh1.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