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- PDB-7xn2: Crystal structure of CvkR, a novel MerR-type transcriptional regulator -

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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 / ATP 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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