[English] 日本語
Yorodumi
- PDB-4xqn: Crystal structure of AgrA LytTR domain in complex with promoters -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xqn
TitleCrystal structure of AgrA LytTR domain in complex with promoters
Components
  • Accessory gene regulator A
  • DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
  • DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
KeywordsDNA/DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA binding / cytoplasm
Similarity search - Function
LytTr DNA-binding domain / : / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LytTr DNA-binding domain / : / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Accessory gene regulator A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsGopal, B. / Rajasree, K.
CitationJournal: Biochem Biophys Rep / Year: 2016
Title: Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression.
Authors: Rajasree, K. / Fasim, A. / Gopal, B.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references / Structure summary
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
C: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
E: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
F: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
H: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
I: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
K: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
L: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
A: Accessory gene regulator A
D: Accessory gene regulator A
G: Accessory gene regulator A
J: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,74121
Polymers78,18212
Non-polymers5599
Water1,53185
1
B: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
C: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
A: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6705
Polymers19,5463
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-14 kcal/mol
Surface area9190 Å2
MethodPISA
2
E: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
F: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
D: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6084
Polymers19,5463
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-12 kcal/mol
Surface area8950 Å2
MethodPISA
3
H: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
I: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
G: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7326
Polymers19,5463
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-13 kcal/mol
Surface area8910 Å2
MethodPISA
4
K: DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
L: DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
J: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7326
Polymers19,5463
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-12 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.170, 61.320, 64.100
Angle α, β, γ (deg.)91.09, 97.48, 94.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
12B
22H
13C
23F
14C
24I
15C
25L
16E
26H
17F
27I
18F
28L
19I
29L
110A
210D
111A
211G
112A
212J
113D
213G
114D
214J
115G
215J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DADADTDTBA5 - 161 - 12
21DADADTDTEC5 - 161 - 12
12DADADTDTBA5 - 161 - 12
22DADADTDTHE5 - 161 - 12
13DADADTDTCB1 - 131 - 13
23DADADTDTFD1 - 131 - 13
14DADADGDGCB2 - 122 - 12
24DADADGDGIF2 - 122 - 12
15DADADGDGCB2 - 122 - 12
25DADADGDGLH2 - 122 - 12
16DADADTDTEC5 - 161 - 12
26DADADTDTHE5 - 161 - 12
17DADADGDGFD2 - 122 - 12
27DADADGDGIF2 - 122 - 12
18DADADGDGFD2 - 122 - 12
28DADADGDGLH2 - 122 - 12
19DADADTDTIF2 - 132 - 13
29DADADTDTLH2 - 132 - 13
110GLUGLULYSLYSAI141 - 2362 - 97
210GLUGLULYSLYSDJ141 - 2362 - 97
111GLUGLULYSLYSAI141 - 2362 - 97
211GLUGLULYSLYSGK141 - 2362 - 97
112GLUGLULYSLYSAI141 - 2362 - 97
212GLUGLULYSLYSJL141 - 2362 - 97
113GLUGLUILEILEDJ141 - 2382 - 99
213GLUGLUILEILEGK141 - 2382 - 99
114GLUGLUILEILEDJ141 - 2382 - 99
214GLUGLUILEILEJL141 - 2382 - 99
115GLUGLUILEILEGK141 - 2382 - 99
215GLUGLUILEILEJL141 - 2382 - 99

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: DNA chain
DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')


Mass: 3694.455 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')


Mass: 3940.595 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Accessory gene regulator A


Mass: 11910.455 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 140-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: agrA, SACOL2026 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYSS / References: UniProt: Q5HEG2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 20% 2-propanol, 20% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.26→44.69 Å / Num. obs: 29349 / % possible obs: 97.1 % / Redundancy: 3.9 % / Rsym value: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.3→44.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.815 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 1465 5 %RANDOM
Rwork0.21127 ---
obs0.21303 27875 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.054 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å2-1.73 Å2-0.65 Å2
2--1.04 Å20.67 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 1983 36 93 5335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0165544
X-RAY DIFFRACTIONr_bond_other_d0.0040.024168
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6017866
X-RAY DIFFRACTIONr_angle_other_deg1.76139601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83423.089191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5971532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024957
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021338
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_it2.8573.9441566
X-RAY DIFFRACTIONr_mcbond_other2.8543.9421565
X-RAY DIFFRACTIONr_mcangle_it4.3885.8981952
X-RAY DIFFRACTIONr_mcangle_other4.3875.9021953
X-RAY DIFFRACTIONr_scbond_it3.5674.7963978
X-RAY DIFFRACTIONr_scbond_other3.5664.7963978
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7257.1435912
X-RAY DIFFRACTIONr_long_range_B_refined10.52142.22722868
X-RAY DIFFRACTIONr_long_range_B_other10.52142.22822869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B38220.01
12E38220.01
21B38200.01
22H38200.01
31C40940.05
32F40940.05
41C33960.05
42I33960.05
51C34160
52L34160
61E38280.01
62H38280.01
71F34280.01
72I34280.01
81F34020.05
82L34020.05
91I37380.05
92L37380.05
101A235720.07
102D235720.07
111A234840.04
112G234840.04
121A236500.04
122J236500.04
131D235500.06
132G235500.06
141D239760.05
142J239760.05
151G240740.05
152J240740.05
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 120 -
Rwork0.255 2054 -
obs--96.28 %

+
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