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- PDB-6jyk: Crystal Structure of C. crescentus free GapR -

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Basic information

Entry
Database: PDB / ID: 6jyk
TitleCrystal Structure of C. crescentus free GapR
ComponentsUPF0335 protein CCNA_03428
KeywordsDNA BINDING PROTEIN / C. crescentus / free / NAPs
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / UPF0335 protein CCNA_03428
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXia, B. / Huang, Q.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: GapR binds DNA through dynamic opening of its tetrameric interface.
Authors: Huang, Q. / Duan, B. / Dong, X. / Fan, S. / Xia, B.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: UPF0335 protein CCNA_03428


Theoretical massNumber of molelcules
Total (without water)11,1961
Polymers11,1961
Non-polymers00
Water1,47782
1
A: UPF0335 protein CCNA_03428

A: UPF0335 protein CCNA_03428


Theoretical massNumber of molelcules
Total (without water)22,3922
Polymers22,3922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.007, 55.007, 110.999
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-111-

HOH

21A-124-

HOH

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Components

#1: Protein UPF0335 protein CCNA_03428 / GapR (growth-associated A/T-binding protein involved in regulation)


Mass: 11195.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: CCNA_03428 / Production host: Escherichia coli (E. coli) / References: UniProt: B8H4R9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.01M Manganese (II) chloride tetrahydrate, 0.1M Sodium citrate (PH 5.6), 2.5M 1,6-Hexanediol and 0.3% v/v Dimethyl sulfoxide
PH range: 5.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→43.8 Å / Num. obs: 13439 / % possible obs: 98 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 37.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 1291

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K2J

6k2j


Resolution: 2→43.776 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1347 10.02 %
Rwork0.2031 --
obs0.204 13439 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms615 0 0 82 697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009617
X-RAY DIFFRACTIONf_angle_d0.891822
X-RAY DIFFRACTIONf_dihedral_angle_d13.029249
X-RAY DIFFRACTIONf_chiral_restr0.03795
X-RAY DIFFRACTIONf_plane_restr0.003106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07160.29831280.2631176X-RAY DIFFRACTION98
2.0716-2.15450.26641300.21471210X-RAY DIFFRACTION100
2.1545-2.25260.2061270.2261166X-RAY DIFFRACTION95
2.2526-2.37130.20561360.19871190X-RAY DIFFRACTION99
2.3713-2.51990.23871320.19941231X-RAY DIFFRACTION100
2.5199-2.71440.24141340.19981198X-RAY DIFFRACTION99
2.7144-2.98750.20841410.20561214X-RAY DIFFRACTION99
2.9875-3.41970.21761330.20241209X-RAY DIFFRACTION97
3.4197-4.30790.19741420.18961206X-RAY DIFFRACTION96
4.3079-43.78670.19671440.20461292X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -14.4973 Å / Origin y: 4.6437 Å / Origin z: -15.1884 Å
111213212223313233
T0.1667 Å2-0.019 Å20.0017 Å2-0.2474 Å2-0.0269 Å2--0.2784 Å2
L0.6047 °2-0.2029 °20.0288 °2-1.0604 °2-0.5549 °2--1.7185 °2
S0.0964 Å °-0.0152 Å °0.0823 Å °0.0536 Å °0.016 Å °-0.0403 Å °-0.0677 Å °0.031 Å °-0.0935 Å °
Refinement TLS groupSelection details: all

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