[English] 日本語
Yorodumi
- PDB-3pmd: Crystal structure of the sporulation inhibitor pXO1-118 from Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pmd
TitleCrystal structure of the sporulation inhibitor pXO1-118 from Bacillus anthracis
ComponentsConserved domain protein
KeywordsLIPID BINDING PROTEIN / globin fold / non-heme globin / sporulation / Bacillus anthracis / kinase sensor domain / chloride coordination / fatty acid-binding protein
Function / homologyHistidine kinase N-terminal domain / Histidine kinase, N-terminal / Histidine kinase N terminal / Globin-like / Orthogonal Bundle / Mainly Alpha / UNDECANOIC ACID / Conserved domain protein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsStranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Insights into Inhibition of Bacillus anthracis Sporulation by a Novel Class of Non-heme Globin Sensor Domains.
Authors: Stranzl, G.R. / Santelli, E. / Bankston, L.A. / La Clair, C. / Bobkov, A. / Schwarzenbacher, R. / Godzik, A. / Perego, M. / Grynberg, M. / Liddington, R.C.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7623
Polymers18,5401
Non-polymers2222
Water1,71195
1
A: Conserved domain protein
hetero molecules

A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5246
Polymers37,0812
Non-polymers4434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5030 Å2
ΔGint-60 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.223, 89.223, 35.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

-
Components

#1: Protein Conserved domain protein / PXO1-118 / Plasmid pX01 (from Bacillus anthracis UM23-1) trans-acting positive regulator (Atx A)


Mass: 18540.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: GBAA_pXO1_0148, pX01-118 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44635
#2: Chemical ChemComp-11A / UNDECANOIC ACID


Mass: 186.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.4
Details: 5% PEG1000, 40% PEG400, 0.1 M TrisHCl, pH 5.4, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9781 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 16351 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038 / Net I/σ(I): 55.1
Reflection shellResolution: 1.76→1.82 Å / Rmerge(I) obs: 0.276 / % possible all: 96

-
Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.063 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22316 830 5 %RANDOM
Rwork0.17792 ---
obs0.1802 15617 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.056 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 14 95 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221394
X-RAY DIFFRACTIONr_bond_other_d0.0010.02972
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.961878
X-RAY DIFFRACTIONr_angle_other_deg1.61232386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9935162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06824.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.496154
X-RAY DIFFRACTIONr_chiral_restr0.070.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7741.5781
X-RAY DIFFRACTIONr_mcbond_other0.6441.5313
X-RAY DIFFRACTIONr_mcangle_it2.99121277
X-RAY DIFFRACTIONr_scbond_it5.1763613
X-RAY DIFFRACTIONr_scangle_it7.7824.5597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.762→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 47 -
Rwork0.23 1134 -
obs--98.66 %
Refinement TLS params.Method: refined / Origin x: -8.038 Å / Origin y: 32.5633 Å / Origin z: 13.4902 Å
111213212223313233
T0.0361 Å2-0.0336 Å2-0.0377 Å2-0.0727 Å20.0195 Å2--0.0801 Å2
L0.7311 °2-0.6387 °2-0.0115 °2-2.2769 °2-0.1456 °2--0.8736 °2
S-0.0576 Å °0.0339 Å °0.1393 Å °0.1743 Å °-0.0342 Å °-0.1115 Å °-0.0908 Å °0.0815 Å °0.0918 Å °

+
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