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- PDB-6wn5: 1.52 Angstrom Resolution Crystal Structure of Transcriptional Reg... -

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Basic information

Entry
Database: PDB / ID: 6wn5
Title1.52 Angstrom Resolution Crystal Structure of Transcriptional Regulator HdfR from Klebsiella pneumoniae
ComponentsTranscriptional regulator HdfR
KeywordsTRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Transcriptional Regulator HdfR
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator HTH, HdfR / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator HdfR / HTH-type transcriptional regulator HdfR
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator HdfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8094
Polymers26,7031
Non-polymers1063
Water3,027168
1
A: Transcriptional regulator HdfR
hetero molecules

A: Transcriptional regulator HdfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6188
Polymers53,4052
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3400 Å2
ΔGint-75 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.389, 62.389, 103.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-301-

CL

21A-457-

HOH

31A-513-

HOH

41A-520-

HOH

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Components

#1: Protein Transcriptional regulator HdfR


Mass: 26702.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: hdfR, B6R99_21715 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE)magic / References: UniProt: A0A657RSZ5, UniProt: W1HWH8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen (PACT, E10): 0.2 M Sodium/Potassium phosphate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: Be
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 32133 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.019 / Rrim(I) all: 0.061 / Rsym value: 0.057 / Χ2: 1.466 / Net I/σ(I): 44.4
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1569 / CC1/2: 0.91 / CC star: 0.976 / Rpim(I) all: 0.263 / Rrim(I) all: 0.827 / Rsym value: 0.783 / Χ2: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→29.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.973 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1656 5.2 %RANDOM
Rwork0.1821 ---
obs0.1833 30411 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.3 Å2 / Biso mean: 26.801 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 1.52→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 3 193 1595
Biso mean--37.04 35.1 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171464
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6362252
X-RAY DIFFRACTIONr_angle_other_deg0.4051.5693427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97123.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81315273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0511510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.021925
X-RAY DIFFRACTIONr_gen_planes_other0.050.02349
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 131 -
Rwork0.241 2183 -
all-2314 -
obs--99.91 %
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)
12.1939-0.59310.39013.81880.51261.402-0.177-0.23730.13270.2360.0276-0.097-0.06910.02440.14940.07530.0258-0.05240.0373-0.01660.048418.850223.026110.0391
23.0173-0.37971.16420.81250.4662.5036-0.3151-0.16560.42290.21390.0685-0.2096-0.31760.10360.24660.14760.001-0.12030.0281-0.02320.137923.31328.636511.7066
30.93840.4650.60543.93872.11872.7149-0.1568-0.06220.05370.41990.11510.03590.2540.07660.04170.11070.0322-0.02860.0563-0.0040.050727.500410.964811.7762
42.6775-0.63240.02592.92030.56532.3814-0.0150.23550.10810.20240.0574-0.20230.08910.0105-0.04240.01570.0039-0.01270.0477-0.00420.017628.87137.403-1.8557
55.6732-0.8354-0.88232.46991.96332.436-0.0582-0.04260.03110.2852-0.01290.17650.2805-0.25690.07110.0844-0.01540.00060.07190.01630.024721.12462.97886.1772
60.69210.28180.7196.34851.76661.4043-0.2176-0.05930.1690.21320.2408-0.3594-0.030.1321-0.02320.14090.0692-0.11360.088-0.06740.102529.302719.54415.9629
71.9975-0.0566-0.52168.62121.07430.8288-0.096-0.5340.18530.3944-0.19350.31820.07530.14550.28950.23350.0549-0.03070.1853-0.05010.190518.701727.319621.6223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 63
2X-RAY DIFFRACTION2A64 - 106
3X-RAY DIFFRACTION3A107 - 128
4X-RAY DIFFRACTION4A129 - 178
5X-RAY DIFFRACTION5A179 - 196
6X-RAY DIFFRACTION6A197 - 214
7X-RAY DIFFRACTION7A215 - 228

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