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- PDB-6ozy: Wild type GapR crystal structure 2 from C. crescentus -

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Basic information

Entry
Database: PDB / ID: 6ozy
TitleWild type GapR crystal structure 2 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: 2.014 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 1.1Sep 22, 2021Group: Data collection / Database references / Category: database_2 / reflns_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2May 22, 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: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9363
Polymers25,8232
Non-polymers1121
Water1,62190
1
A: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319
hetero molecules

A: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8716
Polymers51,6464
Non-polymers2252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10370 Å2
ΔGint-96 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.770, 59.370, 93.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein UPF0335 protein CC_3319


Mass: 12911.602 Da / Num. of mol.: 2
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: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.15 Å3/Da / Density % sol: 42.72 % / Description: Rods
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.4
Details: 0.16 M ammonium sulfate 12 % PEG 3350 10 mM cadmium chloride

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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: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→46.97 Å / Num. obs: 10203 / % possible obs: 66.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 0.5 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 50 / CC1/2: 0.367 / % possible all: 4.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.014→46.97 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.08
RfactorNum. reflection% reflection
Rfree0.2726 528 5.18 %
Rwork0.2331 --
obs0.2352 10198 66.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.29 Å2 / Biso mean: 50.1233 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 2.014→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 1 90 1342
Biso mean--41.9 45.24 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021255
X-RAY DIFFRACTIONf_angle_d0.4281673
X-RAY DIFFRACTIONf_chiral_restr0.02195
X-RAY DIFFRACTIONf_plane_restr0.001215
X-RAY DIFFRACTIONf_dihedral_angle_d10.755507
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0142-2.21690.3255220.268544947113
2.2169-2.53770.2935910.26931944203554
2.5377-3.19710.30041830.26113512369597
3.1971-46.98280.25792320.214237653997100
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)
10.9902-0.7292-0.18895.3994-1.02181.7240.0987-0.253-0.21720.18030.16780.22760.0072-0.041-0.31570.1918-0.0537-0.05990.1476-0.01150.13673.2136-5.088919.361
24.0996-0.1453-1.14715.8144-2.00754.61250.13890.61080.0215-0.1902-0.07560.0056-0.1015-0.2027-0.09060.3156-0.0119-0.02220.20480.07830.1521-1.496317.22857.1658
33.3266-0.56550.43792.6892-1.40747.1485-0.1027-0.35610.04750.5335-0.0604-0.68140.03130.9627-0.11280.3037-0.05270.06460.1522-0.07370.38310.531223.7315-5.9679
41.6598-0.29130.18144.7548-0.33291.34070.14340.11430.1066-0.3486-0.1985-0.8006-0.26760.07010.10040.2136-0.013-0.01540.2435-0.010.15865.84722.138715.0075
54.45670.6152.41060.52080.16171.38140.0064-1.1483-0.27160.29670.07610.0244-0.2154-0.2287-0.17480.36480.02050.04970.390.13640.3839-2.854-23.7084-0.0453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 50 )A11 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 66 )A51 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 87 )A67 - 87
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 68 )B11 - 68
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 89 )B69 - 89

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