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- PDB-1fd9: CRYSTAL STRUCTURE OF THE MACROPHAGE INFECTIVITY POTENTIATOR PROTE... -

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Basic information

Entry
Database: PDB / ID: 1fd9
TitleCRYSTAL STRUCTURE OF THE MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN (MIP) A MAJOR VIRULENCE FACTOR FROM LEGIONELLA PNEUMOPHILA
ComponentsPROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN)
KeywordsISOMERASE / FKBP DOMAIN / LONG ALPHA HELIX / DIMERISATION VIA HELICAL INTERACTIONS
Function / homology
Function and homology information


: / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / protein folding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain / 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 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase ...Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain / 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 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein MIP / Outer membrane protein MIP
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsRiboldi-Tunnicliffe, A. / Jessen, S. / Konig, B. / Rahfeld, J. / Hacker, J. / Fischer, G. / Hilgenfeld, R.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of Mip, a prolylisomerase from Legionella pneumophila
Authors: Riboldi-Tunnicliffe, A. / Konig, B. / Jessen, S. / Weiss, M.S. / Rahfeld, J. / Hacker, J. / Fischer, G. / Hilgenfeld, R.
#1: Journal: Mol.Microbiol. / Year: 1992
Title: Mip protein of Legionella pneumophila exhibits peptidyl-prolyl-cis/trans isomerase (PPlase) activity.
Authors: Fischer, G. / Bang, H. / Ludwig, B. / Mann, K. / Hacker, J.
#2: Journal: FEMS Microbiol.Rev. / Year: 1994
Title: Characterization of Mip proteins of Legionella pneumophila.
Authors: Ludwig, B. / Rahfeld, J. / Schmidt, B. / Mann, K. / Wintermeyer, E. / Fischer, G. / Hacker, J.
#3: Journal: FEBS Lett. / Year: 1995
Title: Small angle X-ray solution scattering study on the dimerization of the FKBP25mem from Legionella pneumophila
Authors: Schmidt, B. / Konig, S. / Svergun, D. / Volkov, V. / Fischer, G. / Koch, M.H.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.4Feb 7, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0003
Polymers22,8691
Non-polymers1312
Water1,72996
1
A: PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN)
hetero molecules

A: PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0006
Polymers45,7382
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3900 Å2
ΔGint-131 kcal/mol
Surface area22940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.750, 80.750, 103.260
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 PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN) / MIP / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / PPIASE / ROTAMASE


Mass: 22869.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: PBLL106 / Production host: Escherichia coli (E. coli)
References: UniProt: P69059, UniProt: Q5ZXE0*PLUS, peptidylprolyl isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.65 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8,000, zinc acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMMES1reservoirpH6.1-6.5
215-20 %(w/v)PEG80001reservoir
3500 mMzinc acetate1reservoir
410 mg/mlprotein1drop
520 mMHEPES1droppH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.279
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 2, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.279 Å / Relative weight: 1
ReflectionResolution: 2.41→22.4 Å / Num. obs: 13545 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 2.58 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.075 / Net I/σ(I): 2.7
Reflection shellResolution: 2.41→2.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.23 / % possible all: 88.2
Reflection
*PLUS
Highest resolution: 2.41 Å / Lowest resolution: 22.4 Å / Num. obs: 10976 / % possible obs: 99.4 % / Redundancy: 4.8 % / Num. measured all: 52836 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.41→22.4 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1089 8 %RANDOM
Rwork0.2302 ---
obs0.2302 13545 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.82 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1-10 Å20 Å20 Å2
2--10 Å20 Å2
3----20 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.41→22.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 2 96 1645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.341.5
X-RAY DIFFRACTIONc_mcangle_it6.972
X-RAY DIFFRACTIONc_scbond_it7.62
X-RAY DIFFRACTIONc_scangle_it9.292.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 161 8.1 %
Rwork0.257 1833 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM_NEW.IONTOPH_NEW.ION
Refinement
*PLUS
Highest resolution: 2.41 Å / Lowest resolution: 22.4 Å / Num. reflection obs: 13169 / σ(F): 0 / Num. reflection Rfree: 1055 / % reflection Rfree: 8 % / Rfactor Rfree: 0.2805
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it5.341.5
X-RAY DIFFRACTIONc_scbond_it7.62
X-RAY DIFFRACTIONc_mcangle_it6.972
X-RAY DIFFRACTIONc_scangle_it9.292.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.257

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