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Entry
Database: PDB / ID: 3w9s
TitleCrystal Structure Analysis of the N-terminal Receiver domain of Response Regulator PmrA
ComponentsOmpR family response regulator in two-component regulatory system with BasS
KeywordsSIGNALING PROTEIN/ANTIMICROBIAL PROTEIN / alpha and beta proteins / Rossmann fold topology / polymyxin b resistant protein A / response regulator / SIGNALING PROTEIN-ANTIMICROBIAL PROTEIN complex
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BERYLLIUM TRIFLUORIDE ION / :
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, C. / Luo, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis of a Physical Blockage Mechanism for the Interaction of Response Regulator PmrA with Connector Protein PmrD from Klebsiella Pneumoniae
Authors: Lou, S.C. / Lou, Y.C. / Rajasekaran, M. / Chang, Y.W. / Hsiao, C.D. / Chen, C.
History
DepositionApr 15, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OmpR family response regulator in two-component regulatory system with BasS
B: OmpR family response regulator in two-component regulatory system with BasS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6966
Polymers29,5162
Non-polymers1814
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: OmpR family response regulator in two-component regulatory system with BasS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8483
Polymers14,7581
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: OmpR family response regulator in two-component regulatory system with BasS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8483
Polymers14,7581
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.994, 49.994, 145.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein OmpR family response regulator in two-component regulatory system with BasS


Mass: 14757.827 Da / Num. of mol.: 2 / Fragment: UNP residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Strain: NTUH-K2044 / Gene: KP1_1760 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: C4X5T7
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Imidazole, 1M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97316 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2008
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97316 Å / Relative weight: 1
ReflectionResolution: 1.7→25.38 Å / Num. all: 38239 / Num. obs: 38222 / % possible obs: 95.1 % / Observed criterion σ(F): 2.0205 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→30 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZES

1zes


Resolution: 1.7→25.38 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1753 1995 5.22 %
Rwork0.1652 --
obs0.1657 38213 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 10 424 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061824
X-RAY DIFFRACTIONf_angle_d1.0922468
X-RAY DIFFRACTIONf_dihedral_angle_d12.453682
X-RAY DIFFRACTIONf_chiral_restr0.076301
X-RAY DIFFRACTIONf_plane_restr0.004317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74050.23651400.20072471X-RAY DIFFRACTION94
1.7405-1.78750.23191450.19452518X-RAY DIFFRACTION94
1.7875-1.84010.18041410.17932558X-RAY DIFFRACTION96
1.8401-1.89950.21821400.17182489X-RAY DIFFRACTION95
1.8995-1.96730.22371300.16562517X-RAY DIFFRACTION95
1.9673-2.04610.16471340.1662521X-RAY DIFFRACTION95
2.0461-2.13910.17431420.16752592X-RAY DIFFRACTION97
2.1391-2.25180.17841440.16492579X-RAY DIFFRACTION98
2.2518-2.39280.17251420.16372644X-RAY DIFFRACTION99
2.3928-2.57740.20551490.17232646X-RAY DIFFRACTION100
2.5774-2.83650.21641470.17422678X-RAY DIFFRACTION100
2.8365-3.24620.17671450.16312653X-RAY DIFFRACTION100
3.2462-4.08710.14731450.15072682X-RAY DIFFRACTION100
4.0871-300.14031510.15962670X-RAY DIFFRACTION99

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