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- PDB-5ked: Structure of the 2.65 Angstrom P2(1) crystal of K. pneumonia MrkH -

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Basic information

Entry
Database: PDB / ID: 5ked
TitleStructure of the 2.65 Angstrom P2(1) crystal of K. pneumonia MrkH
ComponentsFlagellar brake protein YcgR
KeywordsTRANSFERASE / MrkH / biofilm / K. pneumonia
Function / homologypredicted glycosyltransferase like domains / Thrombin, subunit H / nucleotide binding / Beta Barrel / Mainly Beta / Flagellar brake protein YcgR
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSchumacher, M.
CitationJournal: To Be Published
Title: To be released: Structures of K. pneumonia MrkH: dual utilization of the PilZ fold for c-di-GMP and DNA binding by a novel activator of biofilm genes
Authors: Schumacher, M.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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

Downloads & links

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Assembly

Deposited unit
D: Flagellar brake protein YcgR
A: Flagellar brake protein YcgR
B: Flagellar brake protein YcgR
C: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)110,1234
Polymers110,1234
Non-polymers00
Water66737
1
D: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,5311
Polymers27,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,5311
Polymers27,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,5311
Polymers27,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,5311
Polymers27,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Flagellar brake protein YcgR

D: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)55,0612
Polymers55,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4450 Å2
ΔGint2 kcal/mol
Surface area23080 Å2
MethodPISA
6
A: Flagellar brake protein YcgR

C: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)55,0612
Polymers55,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area4260 Å2
ΔGint2 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.512, 207.826, 53.915
Angle α, β, γ (deg.)90.000, 120.170, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer according to size exclusion chromatogrpahy

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Components

#1: Protein
Flagellar brake protein YcgR / Putative glycosyltransferase / Type 3 fimbriae transcription activator


Mass: 27530.670 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mrkH, ycgR, AOT21_03001, PMK1_00755 / Production host: Escherichia coli (E. coli) / References: UniProt: G3FT00
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2 mM MgCl2, 2 mM CaCl2, 0.1 M sodium Hepes pH 7.5, 20% ethylene glycol and 10% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.65→103.913 Å / Num. obs: 27150 / % possible obs: 92.3 % / Redundancy: 3.5 % / Rsym value: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.6 / % possible all: 68.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KGO

5kgo


Resolution: 2.65→45.482 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.86
RfactorNum. reflection% reflection
Rfree0.276 2008 7.42 %
Rwork0.2308 --
obs0.2341 27074 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 56.62 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 193.44 Å2 / Biso mean: 83.15 Å2 / Biso min: 30.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.7565 Å20 Å2-18.9254 Å2
2---16.5906 Å2-0 Å2
3---15.8341 Å2
Refinement stepCycle: final / Resolution: 2.65→45.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7558 0 0 37 7595
Biso mean---57.92 -
Num. residues----914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037692
X-RAY DIFFRACTIONf_angle_d0.62610316
X-RAY DIFFRACTIONf_chiral_restr0.0431142
X-RAY DIFFRACTIONf_plane_restr0.0021320
X-RAY DIFFRACTIONf_dihedral_angle_d14.7182952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.74470.431470.35041721186864
2.7447-2.85460.31111670.30652272243982
2.8546-2.98450.37041830.3172455263889
2.9845-3.14180.4062110.30732538274994
3.1418-3.33860.35242030.29532645284897
3.3386-3.59620.34722250.27142682290798
3.5962-3.9580.27312310.24112630286199
3.958-4.53020.24061980.1852739293799
4.5302-5.70590.22692180.19232713293199
5.7059-45.48840.22712250.20652671289697
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)
11.0003-0.22260.0074-0.27710.1290.1607-0.2303-0.19680.02580.05570.1182-0.17450.2192-0.082600.42690.0020.04070.2777-0.10740.219521.2112-21.9405-18.5395
20.1899-0.0065-0.50371.211.91561.36670.1644-0.0640.29640.00420.1509-0.02090.57770.440700.35790.1386-0.20350.3125-0.07580.268915.4392-9.3066-11.8522
30.83190.45450.07681.2486-0.45450.57720.28710.2222-0.46050.0012-0.61540.398-0.4245-0.0394-00.29410.2417-0.10520.4628-0.23110.51942.267821.3402-1.9824
41.2229-1.3563-0.00180.8484-1.30470.98510.2771-0.3087-0.1103-0.3726-0.03560.245-0.1679-0.1492-00.42170.12770.0020.3582-0.04140.388833.544445.39229.6648
5-0.13560.34720.10550.584-0.64240.1509-0.11680.0457-0.1148-0.3561-0.37060.1924-0.258-0.281200.37980.1215-0.13580.3721-0.30390.322432.2117-10.080714.809
60.7960.60540.50251.271.55541.7858-0.2560.0794-0.1652-0.2793-0.2140.4995-0.12270.051900.31290.0177-0.0250.3396-0.14570.391737.1596-29.15384.7528
70.89850.88010.2943-0.3812-0.26691.61290.2057-0.1034-0.00510.0239-0.4452-0.3375-0.3502-0.239100.54670.12840.12030.23690.04890.41514.931844.34886.8527
80.3136-0.31130.79581.1471.12562.53180.20340.1364-0.02130.05290.3077-0.18620.02460.252800.21410.10370.04180.4731-0.11790.468110.120322.61070.496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:178)A0 - 178
2X-RAY DIFFRACTION2(chain A and resid 179:234)A179 - 234
3X-RAY DIFFRACTION3(chain B and resid 5:114)B5 - 114
4X-RAY DIFFRACTION4(chain B and resid 115:234)B115 - 234
5X-RAY DIFFRACTION5(chain C and resid 5:68)C5 - 68
6X-RAY DIFFRACTION6(chain C and resid 69:234)C69 - 234
7X-RAY DIFFRACTION7(chain D and resid 0:67)D0 - 67
8X-RAY DIFFRACTION8(chain D and resid 68:234)D68 - 234

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