[English] 日本語
Yorodumi
- PDB-7cbv: Crystal structure of the transcriptional regulator PadR from Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cbv
TitleCrystal structure of the transcriptional regulator PadR from Bacillus subtilis (space group H32)
ComponentsPadR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyTranscription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, S.C. / Song, W.S. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Apo structure of the transcriptional regulator PadR from Bacillus subtilis: Structural dynamics and conserved Y70 residue.
Authors: Park, S.C. / Song, W.S. / Yoon, S.I.
History
DepositionJun 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PadR family transcriptional regulator
B: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water1,17165
1
A: PadR family transcriptional regulator

A: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area6780 Å2
ΔGint-50 kcal/mol
Surface area16490 Å2
MethodPISA
2
B: PadR family transcriptional regulator

B: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area6630 Å2
ΔGint-47 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.697, 123.697, 182.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(chain 'A' and ((resid 2 and (name N or name...AA2 - 578 - 63
12LYSLYSSERSER(chain 'A' and ((resid 2 and (name N or name...AA68 - 10974 - 115
13GLNGLNMETMET(chain 'A' and ((resid 2 and (name N or name...AA111 - 139117 - 145
14PROPROASPASP(chain 'A' and ((resid 2 and (name N or name...AA144 - 180150 - 186
25ARGARGARGARG(chain 'B' and (resid 2 through 46 or (resid 47...BB2 - 578 - 63
26LYSLYSSERSER(chain 'B' and (resid 2 through 46 or (resid 47...BB68 - 10974 - 115
27GLNGLNMETMET(chain 'B' and (resid 2 through 46 or (resid 47...BB111 - 139117 - 145
28PROPROASPASP(chain 'B' and (resid 2 through 46 or (resid 47...BB144 - 180150 - 186

-
Components

#1: Protein PadR family transcriptional regulator / PadR


Mass: 21750.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: FIU26_19465 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5F2KJ26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: polyethylene glycol monomethyl ether 5000, sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23965 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2371 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X12

5x12


Resolution: 2.3→29.33 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.0461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 1222 5.11 %
Rwork0.195 22704 -
obs0.1966 23926 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 65 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742732
X-RAY DIFFRACTIONf_angle_d0.90213677
X-RAY DIFFRACTIONf_chiral_restr0.0444404
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d11.10161633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.28421310.24352526X-RAY DIFFRACTION99.77
2.39-2.50.26671220.2242503X-RAY DIFFRACTION99.85
2.5-2.630.27171380.22942518X-RAY DIFFRACTION99.74
2.63-2.80.2611430.21672504X-RAY DIFFRACTION99.77
2.8-3.010.25371560.22012508X-RAY DIFFRACTION99.55
3.01-3.320.28861480.21092502X-RAY DIFFRACTION99.55
3.32-3.80.19421510.18722523X-RAY DIFFRACTION99.15
3.8-4.780.19281170.16262535X-RAY DIFFRACTION98.22
4.78-29.330.19221160.18062585X-RAY DIFFRACTION96.26
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)
13.3750655225-0.114662908423-0.03849451671094.103957237610.4902525321421.80383474423-0.06371336063040.5013268556560.461275974934-0.6359360809810.07893432609350.426609812658-0.219087833146-0.1869854562360.003641743366410.284953795898-0.00739827673855-0.07526754195250.3247215053960.08652823444430.352348801706-11.687166024814.042402574322.4837346752
25.18167479511-1.613462628022.869797183330.998592256725-0.4090045901191.94667300588-0.465042553438-0.2780835480870.3186859800670.401086830982-0.0706432506669-0.210131035359-0.493996637027-0.06928664388120.4411135250710.35273414196-0.0281103215436-0.0338131404870.570942422177-0.09424726375030.475948547294-27.078335396212.63470834237.230374446
32.77743211944-1.643603860410.213907721631.906136140890.3367598682571.586702688830.1318694326590.475854822538-0.197150683335-0.194442869388-0.119771286310.2035702706030.1234021788940.06154883515220.01421022434640.2190897997550.00254105461927-0.03074850521510.247244634829-0.03769768943360.232530233468-44.982779005612.802743062823.2586210327
42.71646075209-1.369947996480.337079095311.46699827879-0.6213351490710.7544898224980.2174142903620.525982797717-0.541758222926-0.205528739338-0.2636426507560.2349192660160.160344012262-0.05955490918360.04475160975920.248402554533-0.00222157620279-0.02726878606090.262039072612-0.08300512306630.294031433681-36.07151580632.4283521397724.7977896502
54.03036102158-0.901285863918-0.1512244420743.28194677641-1.247070908722.79212568268-0.0252040186517-1.019245478460.6170762188190.3342244747110.1053116808640.3207877842840.217881274818-0.768085977503-0.03143642767350.592145834544-0.2351934111880.09271207785430.852227310961-0.1585654856860.642605420933-65.2065930774-18.90634540728.97723304567
60.6738139869330.3419912983280.5769733262485.951001897672.706817590732.284545412410.1698879761210.211296501805-0.545139138088-0.510357119131-0.4692141880090.5164867157270.280531646207-0.3257767690660.1282943896140.476542673042-0.0983520910998-0.07236767944110.545672703666-0.1778852977530.557946974298-56.3795275129-6.93995978328-6.52172844929
70.751436780886-0.3187738209040.5454079639541.84669016536-0.2368199191472.215777632770.114125657219-0.0651808643330.569116703757-0.291345782391-0.508370079990.232475533334-1.21592946456-0.3950271696070.5496357018460.6402321736720.158740403057-0.1338813180290.359344033749-0.02566284634450.449874552114-53.031070387417.1664843647-3.25510700026
82.052653653540.09855864054760.2667960576995.84323607787-0.2601542110695.07723250912-0.0619356883262-0.1786166154470.1983600666430.716085448604-0.00844522049201-0.162198972878-0.320768146204-0.03192604617180.06799821229630.2940840558760.015783511354-0.058737329730.295179652292-0.09484530840290.250450464097-45.5499624958.2015478426310.2213793455
91.48147077270.1667004020880.1504211020864.121038872381.049766853493.1678011366-0.0668075443682-0.140830571255-0.1247296415540.5025120111960.196782748379-0.3349705240680.3414252101170.108368109209-0.04503332320660.3100096729060.0228937786541-0.05877449692440.29402955341-0.06572934240490.321721046919-43.0303446127-3.035056704276.24348381091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 96 )
7X-RAY DIFFRACTION7chain 'B' and (resid 97 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 138 )
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 180 )

+
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