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- PDB-8ruo: D44E mutant crystal structure of LpMIP -

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Basic information

Entry
Database: PDB / ID: 8ruo
TitleD44E mutant crystal structure of LpMIP
ComponentsOuter membrane protein MIP
KeywordsSTRUCTURAL PROTEIN / Mutant / potentiator / stalk helix
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cell outer membrane / protein folding
Similarity search - Function
Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Outer membrane protein MIP
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWiedemann, C. / Whittaker, J.J. / Guskov, A. / Hellmich, U.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: To Be Published
Title: Structure of the LpMIP mutant D44E
Authors: Wiedemann, C. / Whittaker, J.J. / Guskov, A. / Hellmich, U.A.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein MIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6665
Polymers22,1521
Non-polymers5144
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint11 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.185, 77.185, 103.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Outer membrane protein MIP / Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 22152.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: mip / Production host: Escherichia coli (E. coli) / References: UniProt: Q70YI1, peptidylprolyl isomerase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: MES 50mM Magnesium chloride 500mM Zinc chloride 50mM PEG 8000 15%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.54→43.02 Å / Num. obs: 10829 / % possible obs: 99.92 % / Redundancy: 9 % / Biso Wilson estimate: 71.76 Å2 / CC1/2: 0.95 / Net I/σ(I): 13.5
Reflection shellResolution: 2.54→2.631 Å / Num. unique obs: 1047 / CC1/2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→43.02 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.877 / SU B: 15.157 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31851 508 4.7 %RANDOM
Rwork0.25047 ---
obs0.25355 10322 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.023 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.54→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 21 37 1625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121612
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161590
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.8282165
X-RAY DIFFRACTIONr_angle_other_deg0.5861.7653694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4315204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.36153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25710293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02319
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_it5.8226.83819
X-RAY DIFFRACTIONr_mcbond_other5.8146.831819
X-RAY DIFFRACTIONr_mcangle_it8.51612.2811022
X-RAY DIFFRACTIONr_mcangle_other8.51412.2881023
X-RAY DIFFRACTIONr_scbond_it6.7667.45793
X-RAY DIFFRACTIONr_scbond_other6.7627.452794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.23213.3741144
X-RAY DIFFRACTIONr_long_range_B_refined15.59486.261828
X-RAY DIFFRACTIONr_long_range_B_other15.59886.31826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 33 -
Rwork0.395 733 -
obs--100 %

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