[English] 日本語
Yorodumi
- PDB-7pi1: Bacillus subtilis PabB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pi1
TitleBacillus subtilis PabB
ComponentsAminodeoxychorismate synthase component 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / L-tryptophan biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding
Similarity search - Function
Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
Similarity search - Domain/homology
TRYPTOPHAN / Aminodeoxychorismate synthase component 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 Å
AuthorsRooms, L.D. / Race, P.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: To be published
Title: Crystal structure of Bacillus subtilis PabB, component 1.
Authors: Rooms, L.D. / Race, P.R. / Devine, A. / Willis, C.L. / Back, C.R. / Burton, N. / Sudol, A.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Aminodeoxychorismate synthase component 1
BBB: Aminodeoxychorismate synthase component 1
CCC: Aminodeoxychorismate synthase component 1
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,77212
Polymers221,8584
Non-polymers9148
Water20,2491124
1
AAA: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Aminodeoxychorismate synthase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,4641
Non-polymers2292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.084, 170.698, 224.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Aminodeoxychorismate synthase component 1 / ADC synthase / ADCS / 4-amino-4-deoxychorismate synthase component 1


Mass: 55464.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pabB, pab, BSU00740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28820, aminodeoxychorismate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000, 0.01 M tris (base); BICINE, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.729→51.08 Å / Num. obs: 206370 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.094 / Net I/σ(I): 4.4
Reflection shellResolution: 1.729→1.76 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 10035 / CC1/2: 0.256

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model used not yet deposited

Resolution: 1.729→50.826 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.118
RfactorNum. reflection% reflection
Rfree0.236 10342 5.014 %
Rwork0.1989 195901 -
all0.201 --
obs-206243 99.891 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.054 Å2
Refinement stepCycle: LAST / Resolution: 1.729→50.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14629 0 64 1125 15818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01315075
X-RAY DIFFRACTIONr_bond_other_d0.0350.01713809
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.64420372
X-RAY DIFFRACTIONr_angle_other_deg2.3281.57632096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35651832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66422.704847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.073152633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8311592
X-RAY DIFFRACTIONr_chiral_restr0.0670.21930
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216898
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023222
X-RAY DIFFRACTIONr_nbd_refined0.1940.22820
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.212348
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.26799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.21020
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1790.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.240
X-RAY DIFFRACTIONr_nbd_other0.2430.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.229
X-RAY DIFFRACTIONr_mcbond_it2.4763.5027331
X-RAY DIFFRACTIONr_mcbond_other2.4743.5017330
X-RAY DIFFRACTIONr_mcangle_it3.8065.2349138
X-RAY DIFFRACTIONr_mcangle_other3.8065.2359139
X-RAY DIFFRACTIONr_scbond_it3.393.9857744
X-RAY DIFFRACTIONr_scbond_other3.393.9837742
X-RAY DIFFRACTIONr_scangle_it5.5055.79111226
X-RAY DIFFRACTIONr_scangle_other5.5055.79111226
X-RAY DIFFRACTIONr_lrange_it7.63141.25516714
X-RAY DIFFRACTIONr_lrange_other7.57540.90916448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.729-1.7740.3887610.37414115X-RAY DIFFRACTION98.5818
1.774-1.8220.3767280.36814028X-RAY DIFFRACTION99.9932
1.822-1.8750.3626970.36113609X-RAY DIFFRACTION100
1.875-1.9330.3496890.34913154X-RAY DIFFRACTION100
1.933-1.9960.3356970.32612803X-RAY DIFFRACTION100
1.996-2.0660.3096680.29412426X-RAY DIFFRACTION100
2.066-2.1440.2916170.27412029X-RAY DIFFRACTION100
2.144-2.2310.2685990.25111573X-RAY DIFFRACTION100
2.231-2.330.2556100.22511078X-RAY DIFFRACTION100
2.33-2.4430.2435620.20510598X-RAY DIFFRACTION100
2.443-2.5750.2555370.19810113X-RAY DIFFRACTION100
2.575-2.7310.2484890.1889576X-RAY DIFFRACTION100
2.731-2.9190.2144950.1719026X-RAY DIFFRACTION100
2.919-3.1520.2194550.1678426X-RAY DIFFRACTION100
3.152-3.4520.2044050.1617804X-RAY DIFFRACTION100
3.452-3.8570.1973870.157064X-RAY DIFFRACTION100
3.857-4.4490.1752980.1336319X-RAY DIFFRACTION100
4.449-5.4390.182880.1385377X-RAY DIFFRACTION100
5.439-7.6480.2172290.1824250X-RAY DIFFRACTION100
7.648-50.8260.2131310.1772533X-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://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