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- PDB-6ozx: Wild type GapR crystal structure 1 from C. crescentus -

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Basic information

Entry
Database: PDB / ID: 6ozx
TitleWild type GapR crystal structure 1 from C. crescentus
ComponentsUPF0335 protein CC_3319
KeywordsDNA BINDING PROTEIN / DNA-binding / cell-division
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / UPF0335 protein CC_3319
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.851 Å
AuthorsTarry, M. / Harmel, C. / Taylor, J.A. / Marczynski, G.T. / Schmeing, T.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-148472 Canada
Canadian Institutes of Health Research (CIHR)MOP-125998 Canada
CitationJournal: Sci Rep / Year: 2019
Title: Structures of GapR reveal a central channel which could accommodate B-DNA.
Authors: Tarry, M.J. / Harmel, C. / Taylor, J.A. / Marczynski, G.T. / Schmeing, T.M.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 CC_3319


Theoretical massNumber of molelcules
Total (without water)12,9121
Polymers12,9121
Non-polymers00
Water82946
1
A: UPF0335 protein CC_3319

A: UPF0335 protein CC_3319

A: UPF0335 protein CC_3319

A: UPF0335 protein CC_3319


Theoretical massNumber of molelcules
Total (without water)51,6464
Polymers51,6464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation26_555-x,-y+1/2,z1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
Buried area10390 Å2
ΔGint-79 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.481, 116.481, 116.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein UPF0335 protein CC_3319


Mass: 12911.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: CC_3319 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A385
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.55 Å3/Da / Density % sol: 51.77 % / Description: Cubic
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.4
Details: 0.16 M ammonium sulfate 12 % PEG 3350 1 % 1,2-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→82.36 Å / Num. obs: 11872 / % possible obs: 99.9 % / Redundancy: 69.2 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.014 / Rrim(I) all: 0.114 / Net I/σ(I): 30.2 / Num. measured all: 821532 / Scaling rejects: 284
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 54.7 % / Rmerge(I) obs: 2.468 / Num. unique obs: 709 / CC1/2: 0.532 / Rpim(I) all: 0.332 / Rrim(I) all: 2.491 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.851→47.553 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2234 577 4.87 %
Rwork0.1926 --
obs0.194 11843 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.93 Å2 / Biso mean: 47.2682 Å2 / Biso min: 21.74 Å2
Refinement stepCycle: final / Resolution: 1.851→47.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 0 46 673
Biso mean---46.58 -
Num. residues----78
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011629
X-RAY DIFFRACTIONf_angle_d1.209838
X-RAY DIFFRACTIONf_chiral_restr0.04997
X-RAY DIFFRACTIONf_plane_restr0.005108
X-RAY DIFFRACTIONf_dihedral_angle_d13.641255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8505-2.03680.26571380.218327562894
2.0368-2.33150.20351390.170827752914
2.3315-2.93740.24231440.210827922936
2.9374-47.56890.21581560.187929433099
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)
11.6712-0.4898-2.09211.31041.03653.8944-0.1186-0.2366-0.06320.24920.02380.14290.20260.1980.00310.25060.0202-0.00450.24180.02220.2818-12.902714.843121.8465
23.0156-3.00940.35024.3195-0.53140.8307-0.10690.02170.2714-0.19860.16690.1242-0.0796-0.2698-0.06930.28670.03060.03370.2760.01260.3656-4.247619.2652-1.3774
37.28011.2002-1.55472.1195-0.33972.483-0.02830.2231-0.741-0.5309-0.1737-0.04110.3337-0.01060.19520.39090.0506-0.03650.3161-0.05860.373-0.4536.9318-8.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 50 )A12 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 68 )A51 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 89 )A69 - 89

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