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- PDB-8yz7: Crystal structure of DdrI, a CRP family protein from Deinococcus ... -

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Basic information

Entry
Database: PDB / ID: 8yz7
TitleCrystal structure of DdrI, a CRP family protein from Deinococcus radiodurans
ComponentsTranscriptional regulator, FNR/CRP family
KeywordsTRANSCRIPTION / DNA binding / gene regulation
Function / homology:
Function and homology information
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, Y. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222001 China
CitationJournal: Mbio / Year: 2024
Title: cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans.
Authors: Wang, Y. / Hu, J. / Gao, X. / Cao, Y. / Ye, S. / Chen, C. / Wang, L. / Xu, H. / Guo, M. / Zhang, D. / Zhou, R. / Hua, Y. / Zhao, Y.
History
DepositionApr 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, FNR/CRP family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1194
Polymers22,0021
Non-polymers1173
Water1,17165
1
A: Transcriptional regulator, FNR/CRP family
hetero molecules

A: Transcriptional regulator, FNR/CRP family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2398
Polymers44,0042
Non-polymers2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3980 Å2
ΔGint-26 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 87.170, 61.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcriptional regulator, FNR/CRP family


Mass: 22001.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The GenBank accession number A2G07_08515
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Gene: DR_0997 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris, KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 18623 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.075 / Net I/σ(I): 23.77
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.050.61313780.9810.6291
2.05-2.110.61313150.9730.6291
2.11-2.170.42112830.9850.4331
2.17-2.240.34212740.9910.3511
2.24-2.310.33312100.9880.3411
2.31-2.390.22511620.9950.2311
2.39-2.480.17611560.9970.181
2.48-2.580.15210680.9970.1561
2.58-2.70.13310570.9970.1361
2.7-2.830.10710060.9980.111
2.83-2.980.099750.9980.0921
2.98-3.160.0758920.9990.0771
3.16-3.380.0718690.9980.0731
3.38-3.650.0667980.9990.0681
3.65-40.0657490.9980.0671
4-4.470.066660.9990.0611
4.47-5.160.0596090.9990.0611
5.16-6.320.0585180.9990.061
6.32-8.940.054060.9990.0511
8.94-300.0522320.9990.0541

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCW

2zcw


Resolution: 2→30 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 984 5.29 %
Rwork0.2024 --
obs0.2037 18612 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 3 65 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.779
X-RAY DIFFRACTIONf_dihedral_angle_d10.656538
X-RAY DIFFRACTIONf_chiral_restr0.047241
X-RAY DIFFRACTIONf_plane_restr0.006255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.24711430.23452490X-RAY DIFFRACTION100
2.11-2.240.27291360.20822482X-RAY DIFFRACTION100
2.24-2.410.27551220.24772496X-RAY DIFFRACTION100
2.41-2.650.26791750.25162466X-RAY DIFFRACTION100
2.65-3.030.2991450.24212514X-RAY DIFFRACTION100
3.04-3.820.20051290.20052536X-RAY DIFFRACTION100
3.82-25.890.19531340.17332644X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.821 Å / Origin y: -33.502 Å / Origin z: -9.543 Å
111213212223313233
T0.2505 Å20.0063 Å2-0.0114 Å2-0.3147 Å20.0595 Å2--0.2914 Å2
L1.2114 °2-0.5616 °2-0.3249 °2-1.061 °20.8168 °2--1.4875 °2
S0.0101 Å °0.0245 Å °0.1485 Å °-0.0502 Å °-0.0909 Å °-0.0002 Å °-0.0195 Å °0.1453 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 301:303 OR RESID 401:465 ) )A301 - 303
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 301:303 OR RESID 401:465 ) )A401 - 465

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