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- PDB-5kgo: Structure of K. pneumonia MrkH-c-di-GMP complex -

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Basic information

Entry
Database: PDB / ID: 5kgo
TitleStructure of K. pneumonia MrkH-c-di-GMP complex
ComponentsFlagellar brake protein YcgR
KeywordsDNA BINDING PROTEIN / MrkH / biofilm / K. pneumonia / PilZ / TRANSFERASE
Function / homologypredicted glycosyltransferase like domains / Thrombin, subunit H / nucleotide binding / Beta Barrel / Mainly Beta / Chem-C2E / PilZ domain-containing protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.9 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. / Zeng, W.
History
DepositionJun 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6916
Polymers54,9292
Non-polymers2,7624
Water00
1
D: Flagellar brake protein YcgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8453
Polymers27,4651
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Flagellar brake protein YcgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8453
Polymers27,4651
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.573, 74.569, 135.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27464.586 Da / Num. of mol.: 2 / Mutation: H116A, N159D
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: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.1 M Bis tris propane/HCl pH 6.5, 0.2 M sodium fluoride.

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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: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.9→37.285 Å / Num. obs: 14247 / % possible obs: 94.1 % / Redundancy: 3.2 % / Net I/σ(I): 5.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.2 / % possible all: 96.5

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.9→37.285 Å / FOM work R set: 0.7564 / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 1413 10.01 %
Rwork0.2257 12707 -
obs0.2318 14120 92.3 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.733 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 215.32 Å2 / Biso mean: 97.68 Å2 / Biso min: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1--12.8661 Å20 Å2-0 Å2
2--24.9129 Å20 Å2
3----12.0469 Å2
Refinement stepCycle: final / Resolution: 2.9→37.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 184 0 3872
Biso mean--72 --
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0283959
X-RAY DIFFRACTIONf_angle_d1.7215359
X-RAY DIFFRACTIONf_chiral_restr0.06576
X-RAY DIFFRACTIONf_plane_restr0.045655
X-RAY DIFFRACTIONf_dihedral_angle_d40.6881607
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 (%)
2.9-3.00360.36931440.32621288143295
3.0036-3.12380.32271420.2811285142795
3.1238-3.26590.36931420.26311271141396
3.2659-3.4380.32221450.2591308145395
3.438-3.65320.32231370.24171231136891
3.6532-3.9350.32681370.27941240137791
3.935-4.33040.24841420.19141270141292
4.3304-4.95580.20831410.15861270141192
4.9558-6.23910.26621390.20871263140290
6.2391-37.28760.30851440.23151281142587
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)
11.1221.2209-0.42082.1174-0.58851.8395-0.26610.0493-0.59430.4045-0.1712-0.36240.4465-0.300800.6335-0.0511-0.11840.8870.31390.68742.0494-0.151421.6018
22.24121.4982-1.04320.60140.92762.10420.1481-0.9807-0.5920.1997-0.075-0.3414-0.3697-0.37710.00020.43620.0602-0.05480.54540.10580.422533.701614.6006-4.1487
30.7601-0.4852-0.85150.66750.9565-0.03260.00040.2587-0.19160.1833-0.1702-0.3379-1.19880.3901-0.03760.18730.0374-0.05690.7766-0.06670.450924.716315.6358-3.5955
4-0.03830.0560.10610.0606-0.15840.1969-0.7634-0.05280.69090.81990.561.96150.6106-1.654900.7934-0.1729-0.1510.7124-0.11751.198320.58491.2236-4.7368
52.31840.0846-1.4552.9780.92361.486-0.1288-0.21320.5992-0.3386-0.17950.08580.1230.3769-00.36580.166-0.07860.59610.11060.416147.547843.5731-37.9604
62.6197-1.50241.79371.0902-1.55912.1930.199-0.00370.14910.7467-0.3702-1.48420.38550.591-00.5247-0.1134-0.13520.55520.19580.832352.011545.4425-32.8905
73.21810.5474-1.63751.55851.38641.8486-0.1160.29880.24060.09130.0305-0.0756-0.6236-0.0622-00.4731-0.0226-0.00630.3156-0.03390.424440.861219.5113-26.9549
84.93410.8848-0.25830.9962-0.65864.088-0.13840.1541-0.3803-0.34050.1066-0.4723-0.25610.26640.00010.39260.0086-0.05430.2154-0.03310.261241.262318.3516-28.218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:107)A5 - 107
2X-RAY DIFFRACTION2(chain A and resid 108:200)A108 - 200
3X-RAY DIFFRACTION3(chain A and resid 201:219)A201 - 219
4X-RAY DIFFRACTION4(chain A and resid 220:229)A220 - 229
5X-RAY DIFFRACTION5(chain D and resid 5:54)D5 - 54
6X-RAY DIFFRACTION6(chain D and resid 55:107)D55 - 107
7X-RAY DIFFRACTION7(chain D and resid 108:148)D108 - 148
8X-RAY DIFFRACTION8(chain D and resid 149:234)D149 - 234

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