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- PDB-5ejl: MrkH, A novel c-di-GMP dependence transcription regulatory factor. -

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Basic information

Entry
Database: PDB / ID: 5ejl
TitleMrkH, A novel c-di-GMP dependence transcription regulatory factor.
ComponentsKlebsiella pneumoniae genome assembly NOVST
KeywordsDNA BINDING PROTEIN / Complex / c-di-GMP / PilZ domain
Function / homology: / MrkH-like, YcgR-like domain / predicted glycosyltransferase like domains / Thrombin, subunit H / nucleotide binding / Beta Barrel / Mainly Beta / Chem-C2E / Flagellar brake protein YcgR
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWang, F. / Zhu, D. / Gu, L.
CitationJournal: Protein Cell / Year: 2016
Title: The PilZ domain of MrkH represents a novel DNA binding motif
Authors: Wang, F. / He, Q. / Su, K. / Gao, F. / Huang, Y. / Lin, Z. / Zhu, D. / Gu, L.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: Klebsiella pneumoniae genome assembly NOVST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7309
Polymers28,8751
Non-polymers1,8558
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-16 kcal/mol
Surface area13830 Å2
2
A: Klebsiella pneumoniae genome assembly NOVST
hetero molecules

A: Klebsiella pneumoniae genome assembly NOVST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,46018
Polymers57,7502
Non-polymers3,71016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1780 Å2
ΔGint-61 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.556, 68.556, 179.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Klebsiella pneumoniae genome assembly NOVST / Klebsiella pneumoniae genome assembly ST15 / Pilus assembly protein PilZ / Putative ...Klebsiella pneumoniae genome assembly ST15 / Pilus assembly protein PilZ / Putative glycosyltransferase / Type 3 fimbriae transcription activator / Type IV pilus assembly PilZ


Mass: 28875.023 Da / Num. of mol.: 1 / Fragment: uNP residues 1-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: mrkH, AB187_02280, ABY63_13825, KPOL2_01311, KPST15NDM1_03054, PMK1_00755, SE02_15980, SK98_03603, SL05_03385, SL19_03056, SL24_03356, SL48_03379, SL56_02701, SL57_03341, SL69_00334, SL71_ ...Gene: mrkH, AB187_02280, ABY63_13825, KPOL2_01311, KPST15NDM1_03054, PMK1_00755, SE02_15980, SK98_03603, SL05_03385, SL19_03056, SL24_03356, SL48_03379, SL56_02701, SL57_03341, SL69_00334, SL71_01892, SL72_01879, SL84_03450, SL85_03311, SM12_03647, SM17_03206, SM19_03245, SM22_01812, SM40_03226, SM53_03378, SM56_03389, SM59_03130, SM60_03292, SM61_03450, SM63_04027, SM64_03419, SM65_01990, SM67_03796, SM68_03567, SM69_03407, SM70_03107, SM76_03442, SM78_02985, SM80_04811, SM81_03133, SM82_03289, SM83_03401, SM84_02805, SM86_03547, SM88_03405, SM90_03491, SM91_03378, SM92_03536, SM94_03313, SM95_03513, SM96_03441, SM97_03673, SM98_03236, SM99_03225, SN02_03392
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate, Sodium citrate tribasic dihydrate, Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2012
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19898 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rsym value: 0.082 / Net I/σ(I): 31.96
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.54 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1013 5.11 %
Rwork0.2163 --
obs0.2185 19826 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 119 88 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092090
X-RAY DIFFRACTIONf_angle_d0.9752828
X-RAY DIFFRACTIONf_dihedral_angle_d18.11227
X-RAY DIFFRACTIONf_chiral_restr0.058309
X-RAY DIFFRACTIONf_plane_restr0.005344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.42160.29741490.24912620X-RAY DIFFRACTION100
2.4216-2.57330.28581370.23312617X-RAY DIFFRACTION100
2.5733-2.7720.26411540.23222632X-RAY DIFFRACTION100
2.772-3.05080.28461590.23252652X-RAY DIFFRACTION100
3.0508-3.4920.25321300.2232682X-RAY DIFFRACTION100
3.492-4.39840.23211390.19512723X-RAY DIFFRACTION100
4.3984-37.54520.26781450.21272887X-RAY DIFFRACTION100

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