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- PDB-4s05: Crystal structure of Klebsiella pneumoniae PmrA in complex with P... -

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Basic information

Entry
Database: PDB / ID: 4s05
TitleCrystal structure of Klebsiella pneumoniae PmrA in complex with PmrA box DNA
Components
  • (DNA (26-MER)) x 2
  • DNA-binding transcriptional regulator BasR
KeywordsTRANSCRIPTION/DNA / Two-Component System / response regulator / PmrA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA-binding transcriptional regulator BasR / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsHsiao, C.D. / Weng, T.H. / Li, Y.C.
CitationJournal: Nat Commun / Year: 2015
Title: Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA.
Authors: Lou, Y.C. / Weng, T.H. / Li, Y.C. / Kao, Y.F. / Lin, W.F. / Peng, H.L. / Chou, S.H. / Hsiao, C.D. / Chen, C.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding transcriptional regulator BasR
B: DNA-binding transcriptional regulator BasR
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7628
Polymers68,5814
Non-polymers1814
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-57 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.640, 162.640, 131.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA-binding transcriptional regulator BasR


Mass: 26305.926 Da / Num. of mol.: 2 / Mutation: W181G, I220D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: JM45 / Gene: N559_3529 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S5YJU7, UniProt: A0A0R4I965*PLUS
#2: DNA chain DNA (26-MER)


Mass: 7960.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: leading strand / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8009.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: lagging strand / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 7.33 Å3/Da
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 0.1 M CAPS, pH 9.8, 0.8 M Sodium acetate, 12% (w/v) polyethylene glycol 1000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 7, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 19931 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 16.259
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.28 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→29.828 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1997 10.02 %
Rwork0.1783 --
obs0.1833 19930 99.07 %
all-19931 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 1066 10 0 4528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0374715
X-RAY DIFFRACTIONf_angle_d1.4436616
X-RAY DIFFRACTIONf_dihedral_angle_d24.3111844
X-RAY DIFFRACTIONf_chiral_restr0.083760
X-RAY DIFFRACTIONf_plane_restr0.006666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.8960.33261420.30741250X-RAY DIFFRACTION99
3.896-4.00110.36241390.26881264X-RAY DIFFRACTION100
4.0011-4.11860.27551440.24681286X-RAY DIFFRACTION100
4.1186-4.25110.28351370.20851253X-RAY DIFFRACTION99
4.2511-4.40260.22391440.19181271X-RAY DIFFRACTION99
4.4026-4.57830.24931430.17491250X-RAY DIFFRACTION99
4.5783-4.78590.24581420.16211294X-RAY DIFFRACTION99
4.7859-5.03710.19161420.16541268X-RAY DIFFRACTION100
5.0371-5.35090.21081420.17051296X-RAY DIFFRACTION100
5.3509-5.76140.23531460.19341287X-RAY DIFFRACTION100
5.7614-6.33610.23971510.1861298X-RAY DIFFRACTION100
6.3361-7.24150.24181410.18341305X-RAY DIFFRACTION100
7.2415-9.08060.19211410.14091323X-RAY DIFFRACTION100
9.0806-29.82860.20261430.16311288X-RAY DIFFRACTION94
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)
1-0.00920.00620.00250.02250.00860.0161-0.0278-0.0544-0.0609-0.18590.11580.17240.0161-0.01750.32780.1142-0.1719-0.1544-0.2236-0.4704-1.063387.655945.299921.1438
20.15370.00020.05910.8735-0.14120.1209-0.16660.0533-0.2321-0.1408-0.0467-0.26720.02320.0403-0.79570.3759-0.15430.2446-0.0929-0.2070.415102.968226.388313.2902
30.15-0.1062-0.01290.53210.13360.84310.0091-0.2-0.0024-0.07110.206-0.16990.02060.2591.42820.1577-0.06030.07080.3850.0791-0.205296.90437.448544.8908
40.49390.1021-0.23720.70450.39650.7701-0.52080.0582-0.6506-0.3286-0.04190.15470.4642-0.1746-1.13420.9713-0.28240.20240.0954-0.05240.682180.741312.042715.6481
50.1957-0.32920.29070.5502-0.44190.6927-0.04520.04650.0114-0.051-0.1075-0.2379-0.00550.2036-0.33060.7077-0.48560.46810.3261-0.05350.612110.087934.8509-2.7568
60.0540.06440.06450.10.05340.0605-0.06440.096-0.1079-0.38750.0615-0.06760.0759-0.20390.21411.3939-0.4678-0.02160.56-0.15530.885284.93610.7681-4.1061
70.0593-0.0071-0.11630.22550.00310.2274-0.11580.0819-0.0454-0.0746-0.13890.19490.0217-0.14970.00570.8588-0.36240.18110.5324-0.3131.333173.3955-6.6075-1.1255
80.45070.0803-0.03660.0701-0.11820.2746-0.0479-0.0334-0.2501-0.00420.0513-0.0189-0.00640.05270.18290.7065-0.37250.55040.4793-0.15470.835991.10756.9399-7.9175
90.0850.1114-0.11230.377-0.21320.1508-0.0079-0.01130.1142-0.1855-0.1543-0.3917-0.1970.3091-0.24291.0058-0.34090.38330.6419-0.08370.7953108.859732.2121-3.1058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:119 )A1 - 119
2X-RAY DIFFRACTION2( CHAIN A AND RESID 120:219 )A120 - 219
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:104 )B1 - 104
4X-RAY DIFFRACTION4( CHAIN B AND RESID 105:219 )B105 - 219
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:9 )C1 - 9
6X-RAY DIFFRACTION6( CHAIN C AND RESID 10:26 )C10 - 26
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:7 )D1 - 7
8X-RAY DIFFRACTION8( CHAIN D AND RESID 8:14 )D8 - 14
9X-RAY DIFFRACTION9( CHAIN D AND RESID 15:26 )D15 - 26

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