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- PDB-4hn7: Crystal structure of E. coli PmrD -

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Basic information

Entry
Database: PDB / ID: 4hn7
TitleCrystal structure of E. coli PmrD
ComponentsSignal transduction protein pmrD
KeywordsSIGNALING PROTEIN
Function / homologySignal transduction protein PmrD / Polymyxin resistance protein PmrD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #650 / Signal transduction protein PmrD superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / response to antibiotic / Beta Barrel / Mainly Beta / Signal transduction protein PmrD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsJeong, E. / Jung, H. / Ban, C.
CitationJournal: To be Published
Title: Crystal structure of E. coli PmrD
Authors: Jeong, E. / Jung, H. / Ban, C.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transduction protein pmrD


Theoretical massNumber of molelcules
Total (without water)9,8861
Polymers9,8861
Non-polymers00
Water1267
1
A: Signal transduction protein pmrD

A: Signal transduction protein pmrD


Theoretical massNumber of molelcules
Total (without water)19,7712
Polymers19,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.580, 83.580, 75.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Signal transduction protein pmrD / BasR post-transcriptional activator / Polymyxin resistance protein pmrD


Mass: 9885.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2259, JW2254, pmrD / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37590
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50 mM sodium acetate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97959 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2005 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 5617 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.07128.1
2.25-2.37179.1
2.37-2.52197.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JSO

2jso


Resolution: 2.352→16.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.697 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28145 195 4.5 %RANDOM
Rwork0.21109 ---
all0.21435 4370 --
obs0.21435 4111 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.352→16.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 0 7 668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019672
X-RAY DIFFRACTIONr_bond_other_d0.0060.02665
X-RAY DIFFRACTIONr_angle_refined_deg2.161.963904
X-RAY DIFFRACTIONr_angle_other_deg0.9783.0031534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.101584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95625.18527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.85115131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.512153
X-RAY DIFFRACTIONr_chiral_restr0.1140.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02141
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.352→2.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 20 -
Rwork0.334 274 -
obs--92.45 %

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