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- PDB-6ozz: N terminally deleted GapR crystal structure from C. crescentus -

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Basic information

Entry
Database: PDB / ID: 6ozz
TitleN terminally deleted GapR crystal structure 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 / Resolution: 3.304 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319
C: UPF0335 protein CC_3319
D: UPF0335 protein CC_3319
E: UPF0335 protein CC_3319
F: UPF0335 protein CC_3319


Theoretical massNumber of molelcules
Total (without water)70,0406
Polymers70,0406
Non-polymers00
Water00
1
A: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319

A: UPF0335 protein CC_3319
B: UPF0335 protein CC_3319


Theoretical massNumber of molelcules
Total (without water)46,6934
Polymers46,6934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area9930 Å2
ΔGint-87 kcal/mol
Surface area18580 Å2
MethodPISA
2
C: UPF0335 protein CC_3319
D: UPF0335 protein CC_3319
E: UPF0335 protein CC_3319
F: UPF0335 protein CC_3319


Theoretical massNumber of molelcules
Total (without water)46,6934
Polymers46,6934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-91 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.410, 106.410, 139.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA12 - 8724 - 99
2GLUGLUchain BBB12 - 8824 - 100
3GLYGLYchain CCC12 - 8724 - 99
4ILEILEchain DDD12 - 8624 - 98
5GLYGLYchain EEE12 - 8724 - 99
6ILEILEchain FFF12 - 8624 - 98

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Components

#1: Protein
UPF0335 protein CC_3319


Mass: 11673.253 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: C
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

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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: 2.82 Å3/Da / Density % sol: 56.31 % / Description: Elongated arrowheads
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 4 % PEG 3350 0.16 M ammonium sulfate 0.6 % 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: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 9555 / % possible obs: 76.1 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Net I/σ(I): 18
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 1.2 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 49 / CC1/2: 0.88 / % possible all: 5.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.304→49.703 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 43.75
RfactorNum. reflection% reflection
Rfree0.3221 475 4.97 %
Rwork0.2852 --
obs0.2871 9554 76.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 416.6 Å2 / Biso mean: 146.0421 Å2 / Biso min: 21.87 Å2
Refinement stepCycle: final / Resolution: 3.304→49.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 0 0 3661
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033673
X-RAY DIFFRACTIONf_angle_d0.5794892
X-RAY DIFFRACTIONf_chiral_restr0.024565
X-RAY DIFFRACTIONf_plane_restr0.002630
X-RAY DIFFRACTIONf_dihedral_angle_d7.9511490
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2317X-RAY DIFFRACTION1.063TORSIONAL
12B2317X-RAY DIFFRACTION1.063TORSIONAL
13C2317X-RAY DIFFRACTION1.063TORSIONAL
14D2317X-RAY DIFFRACTION1.063TORSIONAL
15E2317X-RAY DIFFRACTION1.063TORSIONAL
16F2317X-RAY DIFFRACTION1.063TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3039-3.78180.4024570.37311055111227
3.7818-4.7640.36881960.31313900409699
4.764-49.70860.29522220.26541244346100
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)
11.91660.2531-1.05522.41383.01065.03510.02960.45410.3003-0.1318-0.47810.039-1.2060.523-0.03211.0068-0.4342-0.23770.90810.10930.592815.399316.704915.8372
27.51350.95541.30764.80050.41085.6037-0.22350.15351.5706-0.1971-0.3713-0.6977-0.25640.29830.27440.50990.1788-0.02080.60140.14370.979920.0699-13.42478.4468
33.5066-0.607-0.42222.63230.09272.8573-0.3472-0.45580.23830.7909-0.14630.69450.2648-0.3671-0.0910.24160.01920.36560.25630.39990.0805-4.2155-6.175318.6242
41.7739-0.16631.90471.16891.81996.6130.36540.0201-1.16180.14110.49890.30820.87661.1642-0.09230.1867-0.0445-0.020.84590.19561.223219.6619-2.5618-2.1897
53.2142-1.13782.86850.3933-1.01452.5196-0.6570.10051.4737-0.18330.1469-1.16080.39110.1394-0.0631.37540.3228-0.57292.06690.14491.427859.1381-17.120423.8836
66.1543-0.3493-0.99466.83280.22236.814-0.32721.55611.23840.0053-0.4694-1.07880.28520.33680.22620.2184-0.0140.04440.905-0.0741.020237.6604-22.27914.6192
73.05421.72511.36624.9779-0.4944.9581-0.0896-0.71260.2333-0.3148-0.2384-1.2216-0.5049-1.16290.52521.36040.14510.24570.67340.02050.656528.3214-36.750717.2648
83.83250.7023.014.92481.17947.21250.2308-1.67960.08750.8285-0.02870.33090.2620.6401-0.29570.49110.05470.24541.6563-0.27680.996833.6507-28.675942.2631
92.38261.0318-2.66334.9741.22474.7051-0.8376-0.11850.71831.39821.12591.3990.19970.2762-0.6120.5920.61310.20161.31130.61581.073126.2719-21.137113.4734
102.0866-2.01961.60581.9767-0.94963.38670.511-0.57390.0181-0.56820.0443-0.73380.5267-1.0749-0.46140.7384-0.0986-0.30181.53750.23881.310853.5986-22.318621.0414
110.5750.0538-0.07741.02720.24080.1853-1.09190.56520.14750.51710.7245-2.25870.2894-0.3170.20521.5454-0.1904-0.09662.8577-0.56331.580154.8502-11.058550.3891
121.4787-1.0127-0.38332.0976-1.25775.5435-0.1598-0.94280.1181-0.05650.35160.51231.1909-1.46510.81890.7593-0.32040.49281.6969-0.411.159126.4604-28.170139.1169
139.4361.2-3.95893.3552-1.00975.45010.41-1.0274-0.12660.1183-0.24510.4707-0.3044-0.58881.02730.8950.3043-0.00632.5327-0.41580.607746.9414-18.679549.4683
140.3501-1.6377-0.75388.39335.84149.0763-0.1759-0.3086-0.11131.6951-0.65270.3720.9172-1.5216-2.53361.1355-0.0756-0.19243.087-0.38750.788462.523-24.904247.1416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 68 )A12 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 87 )A69 - 87
3X-RAY DIFFRACTION3chain 'B' and (resid 12 through 68 )B12 - 68
4X-RAY DIFFRACTION4chain 'B' and (resid 69 through 88 )B69 - 88
5X-RAY DIFFRACTION5chain 'C' and (resid 12 through 51 )C12 - 51
6X-RAY DIFFRACTION6chain 'C' and (resid 52 through 68 )C52 - 68
7X-RAY DIFFRACTION7chain 'C' and (resid 69 through 87 )C69 - 87
8X-RAY DIFFRACTION8chain 'D' and (resid 12 through 68 )D12 - 68
9X-RAY DIFFRACTION9chain 'D' and (resid 69 through 86 )D69 - 86
10X-RAY DIFFRACTION10chain 'E' and (resid 12 through 68 )E12 - 68
11X-RAY DIFFRACTION11chain 'E' and (resid 69 through 87 )E69 - 87
12X-RAY DIFFRACTION12chain 'F' and (resid 12 through 51 )F12 - 51
13X-RAY DIFFRACTION13chain 'F' and (resid 52 through 68 )F52 - 68
14X-RAY DIFFRACTION14chain 'F' and (resid 69 through 86 )F69 - 86

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