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- PDB-4s04: Crystal structure of Klebsiella pneumoniae PmrA in complex with P... -

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Basic information

Entry
Database: PDB / ID: 4s04
TitleCrystal structure of Klebsiella pneumoniae PmrA in complex with PmrA box DNA
Components
  • (DNA (25-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 response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
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: 3.2 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 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 (25-MER)
D: DNA (25-MER)
E: DNA-binding transcriptional regulator BasR
F: DNA-binding transcriptional regulator BasR
G: DNA (25-MER)
H: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,28716
Polymers135,9268
Non-polymers3618
Water1,54986
1
A: DNA-binding transcriptional regulator BasR
B: DNA-binding transcriptional regulator BasR
C: DNA (25-MER)
D: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1438
Polymers67,9634
Non-polymers1814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-67 kcal/mol
Surface area26130 Å2
MethodPISA
2
E: DNA-binding transcriptional regulator BasR
F: DNA-binding transcriptional regulator BasR
G: DNA (25-MER)
H: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1438
Polymers67,9634
Non-polymers1814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-57 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.327, 250.761, 108.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 4 molecules ABEF

#1: Protein
DNA-binding transcriptional regulator BasR


Mass: 26305.926 Da / Num. of mol.: 4 / 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

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DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (25-MER)


Mass: 7630.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: leading strand / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (25-MER)


Mass: 7720.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: lagging strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 94 molecules

#4: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.88 Å3/Da / Density % sol: 74.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl, pH 7.5, 0.8M Ammonium acetate, 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2013
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 38831 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 16.356
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.488 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KpPmrA/26-bp PmrA box complex

Resolution: 3.2→24.194 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2024 5.21 %
Rwork0.1808 --
obs0.1835 38831 45.88 %
all-38831 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→24.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 2050 20 86 9060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129327
X-RAY DIFFRACTIONf_angle_d1.8313010
X-RAY DIFFRACTIONf_dihedral_angle_d23.0713648
X-RAY DIFFRACTIONf_chiral_restr0.0981504
X-RAY DIFFRACTIONf_plane_restr0.0071328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28050.3195390.3523708X-RAY DIFFRACTION12
3.2805-3.36890.4125790.30091429X-RAY DIFFRACTION25
3.3689-3.46780.29751100.29471984X-RAY DIFFRACTION35
3.4678-3.57940.3451330.25382432X-RAY DIFFRACTION42
3.5794-3.70690.29141530.22442774X-RAY DIFFRACTION48
3.7069-3.85470.25361630.20382948X-RAY DIFFRACTION51
3.8547-4.02940.26311630.21372955X-RAY DIFFRACTION52
4.0294-4.24080.24321620.17482961X-RAY DIFFRACTION52
4.2408-4.50490.21661650.14952973X-RAY DIFFRACTION52
4.5049-4.85010.19161640.14082989X-RAY DIFFRACTION52
4.8501-5.33350.22631660.15443003X-RAY DIFFRACTION52
5.3335-6.09450.22931650.1873019X-RAY DIFFRACTION53
6.0945-7.63810.24281760.18863179X-RAY DIFFRACTION56
7.6381-24.19420.16431860.13923453X-RAY DIFFRACTION60
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)
10.24790.10270.23510.17170.12520.4627-0.06470.09030.02-0.05670.037-0.001-0.13890.0905-0.29630.09830.0099-0.08040.1574-0.07130.0193-71.564941.6653-40.1907
20.1111-0.02770.06630.0588-0.00480.07190.03710.0215-0.11960.00150.04260.01360.07510.03910.09790.21450.165-0.07010.1868-0.0570.1352-84.127522.5054-29.521
30.0303-0.0152-0.02770.0562-0.03770.0827-0.02760.2211-0.0834-0.1750.0893-0.05440.0190.2394-0.0010.2897-0.0076-0.05680.5331-0.15750.1557-81.43532.2229-61.3181
40.0549-0.03960.05170.0406-0.07450.2182-0.02290.1117-0.0027-0.0658-0.0342-0.1668-0.12550.1833-0.00781.01260.49120.17550.9123-0.03911.0807-59.95594.9631-30.2656
50.0211-0.00950.00630.0027-0.0030.02240.09880.10860.0409-0.1223-0.0611-0.0457-0.03050.00420.30980.1570.21470.08580.1025-0.0340.0796-55.96-42.8782-2.331
60.2250.00520.00740.0014-0.0030.01320.0455-0.00220.1669-0.0255-0.0346-0.0046-0.0313-0.0109-0.04820.51640.23940.30050.3770.14350.5377-31.7279-37.2873-7.5954
70.1851-0.0896-0.08880.1110.00720.06250.0078-0.15220.1390.00570.0572-0.14040.02980.236-0.25520.18320.02560.10950.241-0.16130.213-47.9636-38.187521.2465
80.0531-0.00580.01610.1978-0.07870.04430.09370.08150.0738-0.00240.00740.0536-0.0845-0.07710.17520.39770.31590.13960.37770.09070.2625-22.1283-65.2941-8.8037
90.02840.04070.00210.2755-0.10810.05780.0065-0.00380.00490.02180.03820.0643-0.0727-0.10060.04140.42650.2575-0.05150.4121-0.03210.2201-90.840532.8616-14.4262
100.00660.00350.00520.03740.00530.0042-0.0241-0.01720.00320.02-0.0005-0.0107-0.009-0.0004-0.03310.45370.22030.03050.32760.07880.33-80.907814.4248-6.7321
110.02510.0176-0.00650.02520.00320.0069-0.0105-0.0384-0.03070.0385-0.0016-0.07240.03330.05730.01010.50810.252-0.10340.4513-0.02260.5488-66.93574.8004-14.5078
120.0112-0.003-0.00710.00240.0030.0152-0.03420.0188-0.01070.0572-0.0368-0.0088-0.0193-0.0128-0.01920.92160.45740.02030.63330.0151.0144-55.5758-12.0818-14.7102
130.02390.02290.03060.06820.02440.04-0.07690.01790.1218-0.0159-0.04490.0135-0.1145-0.0125-0.00860.57230.23450.01380.36810.10640.6991-38.6369-22.9183-20.1359
140.0920.00320.03010.0629-0.00150.03660.1130.14690.1157-0.05980.00560.0007-0.1061-0.04790.19970.68260.41040.29290.7330.26510.6004-14.1177-55.2716-24.3024
150.0010.00250.00020.0084-0.01260.0849-0.04590.00710.01090.0722-0.0488-0.02810.01020.0427-0.02940.71720.3902-0.02170.6050.02511.0369-54-8.7334-17.9872
160.0227-0.03210.00490.0460.00370.0817-0.0525-0.0655-0.20380.0359-0.0361-0.07190.07310.0453-0.10940.610.3239-0.0960.47420.01340.5825-69.93895.6993-10.0428
170.0387-0.0118-0.04390.0702-0.01410.0606-0.0781-0.0801-0.01740.10870.0190.09850.0292-0.004-0.11610.55420.30160.02730.43870.00360.3081-89.324930.0665-12.6452
180.04170.0138-0.01360.0269-0.01210.00710.11430.14760.1107-0.09930.0007-0.0543-0.1256-0.03990.07450.59590.33010.19540.53070.15770.5023-8.6821-63.883-22.7415
190.2261-0.054-0.00560.01330.00710.1983-0.05330.03430.1029-0.0752-0.09790.0729-0.0874-0.0749-0.09640.7040.35130.28870.60580.25610.7583-32.6846-32.3822-24.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:120 )A1 - 120
2X-RAY DIFFRACTION2( CHAIN A AND RESID 121:219 )A121 - 219
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:119 )B1 - 119
4X-RAY DIFFRACTION4( CHAIN B AND RESID 120:219 )B120 - 219
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:119 )E1 - 119
6X-RAY DIFFRACTION6( CHAIN E AND RESID 120:219 )E120 - 219
7X-RAY DIFFRACTION7( CHAIN F AND RESID 1:119 )F1 - 119
8X-RAY DIFFRACTION8( CHAIN F AND RESID 120:219 )F120 - 219
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:8 )C1 - 8
10X-RAY DIFFRACTION10( CHAIN C AND RESID 9:13 )C9 - 13
11X-RAY DIFFRACTION11( CHAIN C AND RESID 14:18 )C14 - 18
12X-RAY DIFFRACTION12( CHAIN C AND RESID 19:25 )C19 - 25
13X-RAY DIFFRACTION13( CHAIN G AND RESID 1:6 )G1 - 6
14X-RAY DIFFRACTION14( CHAIN G AND RESID 7:25 )G7 - 25
15X-RAY DIFFRACTION15( CHAIN D AND RESID 1:6 )D1 - 6
16X-RAY DIFFRACTION16( CHAIN D AND RESID 7:14 )D7 - 14
17X-RAY DIFFRACTION17( CHAIN D AND RESID 15:25 )D15 - 25
18X-RAY DIFFRACTION18( CHAIN H AND RESID 1:11 )H1 - 11
19X-RAY DIFFRACTION19( CHAIN H AND RESID 12:25 )H12 - 25

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