[English] 日本語
Yorodumi
- PDB-7xn2: Crystal structure of CvkR, a novel MerR-type transcriptional regulator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xn2
TitleCrystal structure of CvkR, a novel MerR-type transcriptional regulator
ComponentsAlr3614 protein
KeywordsTRANSCRIPTION / MerR-type transcriptional regulator
Function / homologyMerR HTH family regulatory protein / MerR-type HTH domain / Putative DNA-binding domain superfamily / regulation of DNA-templated transcription / DNA binding / ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Alr3614 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLiang, Y.J. / Zhu, T. / Ma, H.L. / Lu, X.F. / Hess, W.R.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0909700 China
National Science Foundation (NSF, China)M-0214 China
National Natural Science Foundation of China (NSFC)31525002 China
National Natural Science Foundation of China (NSFC)31570068 China
National Natural Science Foundation of China (NSFC)31761133008 China
CitationJournal: Nat Commun / Year: 2023
Title: CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems.
Authors: Ziemann, M. / Reimann, V. / Liang, Y. / Shi, Y. / Ma, H. / Xie, Y. / Li, H. / Zhu, T. / Lu, X. / Hess, W.R.
History
DepositionApr 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alr3614 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3623
Polymers17,7481
Non-polymers6132
Water1,65792
1
A: Alr3614 protein
hetero molecules

A: Alr3614 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7236
Polymers35,4972
Non-polymers1,2274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3130 Å2
ΔGint-16 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.579, 49.703, 40.520
Angle α, β, γ (deg.)90.000, 116.040, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Alr3614 protein / CvkR


Mass: 17748.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr3614 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YR38
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 0.1 M phosphate citrate, 15% PEG300, 10 mM ATP / PH range: 4.4-4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 18581 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.061 / Χ2: 1.464 / Net I/σ(I): 7.8 / Num. measured all: 89996
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6650.44118300.8770.2110.4910.752100
1.66-1.724.90.36418520.9020.1760.4060.845100
1.72-1.84.80.28318410.9330.1380.3161.299.9
1.8-1.94.50.2218450.9520.1120.2481.4699.7
1.9-2.024.90.19218660.9640.0930.2142.16799.9
2.02-2.174.90.15218270.970.0740.172.4699.8
2.17-2.394.70.10818680.9880.0540.1212.21799.8
2.39-2.7450.07818750.9920.0380.0871.553100
2.74-3.454.80.0518580.9970.0250.0561.126100
3.45-504.90.03719190.9970.0180.0410.89699.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→24.24 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 964 5.19 %
Rwork0.1941 17606 -
obs0.1953 18570 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.77 Å2 / Biso mean: 45.7662 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 1.6→24.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 38 92 1329
Biso mean--43.5 51.62 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.680.34431410.27552463260498
1.68-1.790.2711300.253625192649100
1.79-1.930.26251350.223624872622100
1.93-2.120.23261440.217325232667100
2.12-2.430.23281440.203324882632100
2.43-3.060.23021480.204525322680100
3.06-24.240.18481220.170625942716100
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)
13.67121.71790.57351.0407-0.49752.6048-0.97481.4051-0.8784-0.73630.534-0.84560.3646-0.1372-0.28640.5039-0.38950.06090.9657-0.21890.1152-26.0735-12.07961.0812
22.8641-0.6675-2.11173.2622-0.64742.1412-0.46660.4064-1.1156-0.51280.0878-0.95661.07870.86440.16750.41220.01170.07240.4423-0.17570.5163-19.4698-18.341510.6365
30.6715-0.99671.38312.6387-0.42755.2155-0.06530.8966-0.9457-0.08310.3176-0.36790.61790.72830.12160.3318-0.02020.0120.3761-0.15230.4047-30.5841-19.765611.057
42.7068-0.30450.66314.29230.22422.5743-0.44391.0595-0.2977-0.10860.2298-0.04590.2343-0.22910.1960.3011-0.10530.03620.4001-0.06550.2162-25.094-11.38667.2492
56.1942-3.0182-0.88686.59450.42723.7446-0.28340.084-0.18250.37670.22720.15390.2886-0.29050.0990.2337-0.0257-0.02250.20050.0120.3281-20.7937-6.289820.0768
64.0972-1.662-3.12263.2056-1.11516.9406-0.17861.16080.7042-0.54190.05861.4322-0.4912-1.87630.57270.31060.0448-0.03740.52130.10150.6353-32.01822.746613.2844
76.2027-0.3541-0.74156.82670.65196.78790.02120.73650.0482-0.65460.05351.1397-0.3944-0.8851-0.13620.24040.0327-0.07570.34240.05710.3342-22.99627.886614.6021
87.10523.9227-3.41286.12080.31895.97790.6437-2.1703-1.69670.9863-0.06360.27320.7185-0.4917-0.14740.7076-0.00660.04260.83130.18830.6457-14.4107-3.536531.4007
96.9101-0.54782.42462.49690.11423.7674-0.0956-0.1750.42080.06990.16570.1208-0.31-0.0389-0.00480.23270.01410.01940.1650.02110.2393-14.01469.375320.8807
100.14960.01980.24463.04333.29144.3263-1.18391.86041.1457-1.96921.64790.6003-0.9625-0.17080.24830.7174-0.4387-0.13951.03760.23870.1714-25.37440.25590.3176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )A3 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )A19 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 38 )A29 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 63 )A39 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 80 )A64 - 80
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 90 )A81 - 90
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 101 )A91 - 101
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 108 )A102 - 108
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 133 )A109 - 133
10X-RAY DIFFRACTION10chain 'A' and (resid 134 through 150 )A134 - 150

+
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