[English] 日本語
Yorodumi
- PDB-3onq: Crystal Structure of Regulator of Polyketide Synthase Expression ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3onq
TitleCrystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis
ComponentsRegulator of polyketide synthase expression
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / helix-bundle / alpha-beta-alpha sandwich / Signal transduction / cytosol
Function / homology
Function and homology information


PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5100 / Alpha-Beta Plaits - #2730 / PucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / : / PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits ...PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5100 / Alpha-Beta Plaits - #2730 / PucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / : / PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PucR C-terminal helix-turn-helix domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.098 Å
AuthorsKim, Y. / Wu, R. / Tan, K. / Morales, J. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis
Authors: Kim, Y. / Wu, R. / Tan, K. / Morales, J. / Bearden, J. / Joachimiak, A.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Regulator of polyketide synthase expression
B: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00139
Polymers115,6864
Non-polymers3,31535
Water14,142785
1
A: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
hetero molecules

B: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00139
Polymers115,6864
Non-polymers3,31535
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area13070 Å2
ΔGint-325 kcal/mol
Surface area43370 Å2
MethodPISA
2
A: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,73622
Polymers57,8432
Non-polymers1,89320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-170 kcal/mol
Surface area23140 Å2
MethodPISA
3
B: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,26417
Polymers57,8432
Non-polymers1,42115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-135 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.452, 93.452, 166.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Regulator of polyketide synthase expression


Mass: 28921.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (bacteria)
Strain: ATCC 15703 / Gene: BAD_0249 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: A0ZZZ7
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris-Propane:NaOH pH 7.0, 1.5 M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 22, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 78815 / Num. obs: 78815 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 31.69 Å2 / Rsym value: 0.105 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4 / Num. unique all: 3908 / Rsym value: 0.725 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.098→39.811 Å / SU ML: 0.3 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3901 5.05 %random
Rwork0.173 ---
all0.175 77313 --
obs0.175 77313 98.16 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.213 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.5917 Å20 Å20 Å2
2--3.7708 Å2-0 Å2
3---0.8209 Å2
Refinement stepCycle: LAST / Resolution: 2.098→39.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 187 785 8589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087974
X-RAY DIFFRACTIONf_angle_d1.03610867
X-RAY DIFFRACTIONf_dihedral_angle_d13.1872892
X-RAY DIFFRACTIONf_chiral_restr0.0721247
X-RAY DIFFRACTIONf_plane_restr0.0061399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0983-2.17320.25943820.20417210759298
2.1732-2.26020.26513800.21437177755797
2.2602-2.36310.25773870.21167090747796
2.3631-2.48770.25083760.19567215759197
2.4877-2.64350.22523510.19667280763197
2.6435-2.84760.24313910.19267281767298
2.8476-3.1340.22834020.18737366776899
3.134-3.58730.19844010.177674667867100
3.5873-4.51860.16023980.137475327930100
4.5186-39.81790.16944330.157977958228100
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)
10.2740.10760.00360.7442-0.83111.50150.08150.0273-0.1606-0.16980.08950.10560.2863-0.1519-0.16150.2336-0.0443-0.04860.18160.04480.249147.8729.783559.5799
21.0334-0.49560.16480.3346-0.01390.6783-0.03290.1541-0.0854-0.0031-0.01750.0298-0.0166-0.07960.04990.1297-0.01330.01670.1742-0.02470.1361.126714.070520.8336
30.62510.13610.02530.626-0.10380.46960.049-0.0704-0.08070.02-0.0481-0.0124-0.0288-0.014-0.00390.16440.00110.00310.18530.03550.184466.295647.803572.4027
40.69070.3007-0.81810.7996-0.34841.2525-0.0357-0.2316-0.03050.0637-0.011-0.00540.08620.34490.04350.210.0128-0.02090.27860.0170.204770.53966.034346.2661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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