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- PDB-5kec: Structure of K. pneumonia MrkH in its apo state. -

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Basic information

Entry
Database: PDB / ID: 5kec
TitleStructure of K. pneumonia MrkH in its apo state.
ComponentsFlagellar brake protein YcgR
KeywordsDNA BINDING PROTEIN / MrkH / K. pneumonia / biofilm / c-di-GMP / TRANSFERASE
Function / homology: / MrkH-like, YcgR-like domain / predicted 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: 1.949 Å
AuthorsSchumacher, M.
CitationJournal: To Be Published
Title: to be published: 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


Theoretical massNumber of molelcules
Total (without water)55,6022
Polymers55,6022
Non-polymers00
Water2,702150
1
A: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Flagellar brake protein YcgR


Theoretical massNumber of molelcules
Total (without water)27,8011
Polymers27,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint6 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.800, 93.450, 206.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsMonomer according to size exclusion chromatogrpahy and crosslinking

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Components

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


Mass: 27801.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: contains N-terminal GSH leftover from thrombin cleavage as a pET15b expressed protein.
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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 600, 0.1 M Hepes pH 7.5, 50 mM lithium sulphate, 10% w/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.949→45.571 Å / Num. obs: 29115 / % possible obs: 90.4 % / Redundancy: 2.7 % / CC1/2: 0.995 / Rsym value: 0.073 / Net I/σ(I): 7.2
Reflection shellResolution: 1.949→2.07 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 3626 / CC1/2: 0.647 / Rsym value: 0.551 / % possible all: 79.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5ked


Resolution: 1.949→42.565 Å / FOM work R set: 0.8142 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 2000 6.87 %
Rwork0.2027 27115 -
obs0.2055 29115 90.39 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.354 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 41.62 Å2 / Biso min: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-6.2168 Å20 Å20 Å2
2---11.0576 Å20 Å2
3---4.8409 Å2
Refinement stepCycle: final / Resolution: 1.949→42.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 150 3912
Biso mean---41.12 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053828
X-RAY DIFFRACTIONf_angle_d0.7995132
X-RAY DIFFRACTIONf_chiral_restr0.055568
X-RAY DIFFRACTIONf_plane_restr0.002656
X-RAY DIFFRACTIONf_dihedral_angle_d14.1861470
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 (%)
1.949-2.01870.36311650.30382228239376
2.0187-2.09950.28251830.25482483266684
2.0995-2.19510.2861910.22422599279088
2.1951-2.31080.29671900.22522580277087
2.3108-2.45560.31461950.21822650284589
2.4556-2.64510.26512020.21192730293292
2.6451-2.91130.27122070.21892814302194
2.9113-3.33240.25252160.1972926314297
3.3324-4.19790.22062220.17883005322799
4.1979-42.57560.19982290.19243100332997
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)
10.01120.0177-0.02220.00480.0077-0.00170.28290.62580.34860.6262-0.32530.17340.23870.0536-00.27780.00980.01560.3005-0.0620.223943.712529.2543-1.7235
20.19860.0143-0.230.51420.26140.1212-0.03020.0818-0.0623-0.01360.0443-0.0433-0.0911-0.0805-00.1344-0.02960.00510.1534-0.0040.137725.963129.726411.9296
30.33640.37480.05750.38720.14780.3214-0.0768-0.0883-0.03760.0869-0.10040.0575-0.1620.0276-00.192-0.02730.06620.1705-0.00430.206725.376331.461418.0104
4-0.02440.17870.13160.10290.0385-0.0285-0.2334-0.0699-0.1066-0.00880.2459-0.30390.0179-0.110100.3044-0.0128-0.050.26340.00340.319240.911724.848832.1739
50.68370.4288-0.19120.59290.48770.3666-0.01760.02760.0472-0.08750.03130.0949-0.03860.0217-00.1125-0.00850.010.1386-0.01250.110439.623333.808641.278
60.46340.1072-0.74480.2901-0.17840.686-0.1311-0.0009-0.1122-0.07230.0658-0.1578-0.03890.143800.1888-0.03460.02130.13730.00040.144433.758310.120936.9216
70.0729-0.2641-0.25610.1773-0.02070.145-0.12880.08530.0177-0.0005-0.04440.0706-0.0066-0.012300.2019-0.01830.0130.1437-0.02580.202224.877115.254439.4565
80.63590.19490.18330.54730.08830.4838-0.03920.00940.0023-0.044-0.10380.10910.12110.003200.155-0.04420.02820.1501-0.02090.180428.528611.82533.6351
90.07210.5606-0.37140.9339-0.17580.65220.04470.12790.16160.1865-0.01380.09850.0668-0.012300.1277-0.01960.03460.158-0.03110.142810.65719.308512.4555
100.5860.2009-0.0640.51620.48630.45070.0379-0.0590.06090.12250.0102-0.0520.08850.004400.17620.0014-0.00390.12940.01230.1519.51269.030212.4484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:6)A0 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:54)A7 - 54
3X-RAY DIFFRACTION3(chain A and resid 55:108)A55 - 108
4X-RAY DIFFRACTION4(chain A and resid 109:120)A109 - 120
5X-RAY DIFFRACTION5(chain A and resid 121:234)A121 - 234
6X-RAY DIFFRACTION6(chain D and resid 5:37)D5 - 37
7X-RAY DIFFRACTION7(chain D and resid 38:65)D38 - 65
8X-RAY DIFFRACTION8(chain D and resid 66:115)D66 - 115
9X-RAY DIFFRACTION9(chain D and resid 116:184)D116 - 184
10X-RAY DIFFRACTION10(chain D and resid 185:234)D185 - 234

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