[English] 日本語
Yorodumi
- PDB-5ewb: Racemic crystal structures of Pribnow box consensus promoter sequ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ewb
TitleRacemic crystal structures of Pribnow box consensus promoter sequence (P21/c)
Components
  • PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND
  • PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
KeywordsDNA / Racemic DNA crystallography / Pribnow box / Bacterial Promoter / B-DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / Srivastava, S.C. / Huc, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-320892 France
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.
Authors: Mandal, P.K. / Collie, G.W. / Srivastava, S.C. / Kauffmann, B. / Huc, I.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
B: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND
C: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
D: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)14,6504
Polymers14,6504
Non-polymers00
Water1,51384
1
A: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
B: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
D: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.118, 67.115, 47.860
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number14
Space group name H-MP121/c1

-
Components

#1: DNA chain PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Pribnow box consensus sequence TATAAT / Source: (synth.) synthetic construct (others)
#2: DNA chain PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Racemic DNA mixture*, sodium cacodylate, sodium chloride, potassium chloride, spermine tetrahydrochloride, MPD *For crystallization, four strands were used i.e. (1) d(CGCTATAATGCG) with L- ...Details: Racemic DNA mixture*, sodium cacodylate, sodium chloride, potassium chloride, spermine tetrahydrochloride, MPD *For crystallization, four strands were used i.e. (1) d(CGCTATAATGCG) with L-sugars; (2) d(CGCATTATAGCG) with L-sugars; (3) d(CGCTATAATGCG) with D-sugars and (4) d(CGCATTATAGCG) with D-sugars. Enantio-pure DNA solutions were prepared between the non-self complementary strands. Enantiopure DNA solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.69→42.6 Å / Num. obs: 29346 / % possible obs: 99.3 % / Redundancy: 6.56 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.64
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 6.42 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.02 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQ2

1fq2


Resolution: 1.694→42.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3496 1431 4.9 %Random selection
Rwork0.2988 ---
obs0.3012 29228 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.694→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 0 84 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081088
X-RAY DIFFRACTIONf_angle_d1.0121672
X-RAY DIFFRACTIONf_dihedral_angle_d32.169464
X-RAY DIFFRACTIONf_chiral_restr0.052188
X-RAY DIFFRACTIONf_plane_restr0.01148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.694-1.75460.48351270.45212679X-RAY DIFFRACTION95
1.7546-1.82480.44771500.42632763X-RAY DIFFRACTION99
1.8248-1.90790.44471430.41532794X-RAY DIFFRACTION100
1.9079-2.00850.43111490.42572787X-RAY DIFFRACTION100
2.0085-2.13430.46761540.38112780X-RAY DIFFRACTION100
2.1343-2.29910.47371300.35712824X-RAY DIFFRACTION100
2.2991-2.53040.34921740.35762778X-RAY DIFFRACTION100
2.5304-2.89650.42281310.35742817X-RAY DIFFRACTION100
2.8965-3.6490.33971420.30932762X-RAY DIFFRACTION99
3.649-42.61540.25881310.20642813X-RAY DIFFRACTION100
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)
12.38240.14010.27383.4968-0.22372.9191-0.35680.13610.5486-0.4487-0.31750.481-0.435-0.39770.54750.38390.0712-0.11040.3974-0.06420.481645.23144.65528.5881
26.3926-2.28912.31527.9204-0.31822.0659-0.05760.41470.46090.4967-0.3429-0.66050.2567-0.01180.43090.40180.0060.01980.3726-0.05420.334544.067723.257617.0321
31.2453-1.17250.98542.5756-0.36610.97380.28140.318-0.2248-0.3626-0.3686-0.11640.18920.17970.10870.44250.05680.01480.3673-0.03530.364740.637224.465813.5866
40.959-1.3154-0.57728.11293.53097.97990.0566-0.08470.42570.4981-0.6462-0.0582-0.2852-0.76850.4840.38560.0643-0.09440.4253-0.00350.442847.18044.565516.2136
51.6207-0.00370.73333.36270.53072.9582-0.21350.16370.6310.1282-0.10650.3205-0.3288-0.33790.4150.32840.06170.01580.3442-0.02080.405258.82087.434132.0831
62.8336-1.14511.06835.0095-0.46953.0532-0.03320.29450.01790.3084-0.3086-0.98840.20930.19130.33740.35440.01010.10490.3912-0.03480.528858.66225.837639.4618
70.8202-0.40770.98332.5626-0.05521.24240.04030.4262-0.2991-0.6196-0.1719-0.4185-0.05120.11110.110.35370.02790.09060.3694-0.03930.385555.551827.200536.1033
84.0124-0.15740.43066.98912.4528.04240.0174-0.62280.6630.9088-0.2403-0.63240.5027-0.55860.28040.42730.0649-0.03110.3741-0.01570.418860.50926.942539.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 12 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 12 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'C' and (resid 6 through 12 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 12 )

+
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