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- PDB-7dwm: Crystal structure of the phage VqmA-DPO complex -

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Basic information

Entry
Database: PDB / ID: 7dwm
TitleCrystal structure of the phage VqmA-DPO complex
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION / VqmA / 3 / 5-dimethylpyrazin-2-ol(DPO) / bacteriophage VP882
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
PAS fold-4 / PAS fold / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
3,5-dimethylpyrazin-2-ol / Transcriptional regulator
Similarity search - Component
Biological speciesVibrio virus VP882
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGu, Y. / Yang, W.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870737 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Understanding the mechanism of asymmetric gene regulation determined by the VqmA of vibriophage.
Authors: Gu, Y. / Zhi, S.X. / Yang, N. / Yang, W.S.
History
DepositionJan 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5194
Polymers53,2712
Non-polymers2482
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-36 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.664, 133.664, 89.514
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation / VqmA


Mass: 26635.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio virus VP882 / Production host: Escherichia coli (E. coli) / References: UniProt: A2I306
#2: Chemical ChemComp-A1U / 3,5-dimethylpyrazin-2-ol


Mass: 124.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M TRIS hydrochloride pH 7.2, 0.005 M Magnesium sulfate hydrate, 2.4 M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979106 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979106 Å / Relative weight: 1
ReflectionResolution: 2.65→115.76 Å / Num. obs: 25381 / % possible obs: 93.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 75.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2882 / CC1/2: 0.789 / Rpim(I) all: 0.323 / Rrim(I) all: 0.979

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IDE

6ide


Resolution: 2.65→35.43 Å / SU ML: 0.4424 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2907 2005 7.92 %
Rwork0.257 23322 -
obs0.2598 25327 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.91 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 18 24 3507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643550
X-RAY DIFFRACTIONf_angle_d1.11344782
X-RAY DIFFRACTIONf_chiral_restr0.24522
X-RAY DIFFRACTIONf_plane_restr0.0077621
X-RAY DIFFRACTIONf_dihedral_angle_d30.3031326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.3777980.35471120X-RAY DIFFRACTION63.67
2.72-2.790.35111500.32471782X-RAY DIFFRACTION100
2.79-2.870.35261470.3221768X-RAY DIFFRACTION100
2.87-2.960.38561490.35151753X-RAY DIFFRACTION100
2.96-3.070.39421500.35191758X-RAY DIFFRACTION100
3.07-3.190.3931540.31471786X-RAY DIFFRACTION100
3.19-3.340.37251510.30221768X-RAY DIFFRACTION100
3.34-3.510.35451230.29171396X-RAY DIFFRACTION79.4
3.51-3.730.33161200.28871405X-RAY DIFFRACTION78.53
3.73-4.020.28281300.25221527X-RAY DIFFRACTION85.72
4.02-4.430.24711530.22371786X-RAY DIFFRACTION100
4.43-5.060.26231570.22971806X-RAY DIFFRACTION100
5.07-6.370.29711600.27551813X-RAY DIFFRACTION100
6.38-35.430.23181630.2011854X-RAY DIFFRACTION98.87

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