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- PDB-2y4x: Structure of a domain from the type IV pilus biogenesis lipoprote... -

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Basic information

Entry
Database: PDB / ID: 2y4x
TitleStructure of a domain from the type IV pilus biogenesis lipoprotein PilP, from Pseudomonas aeruginosa PA01
ComponentsPILP PROTEIN
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus / type IV pilus-dependent motility / plasma membrane
Similarity search - Function
SH3 type barrels. - #830 / Type IV pilus inner membrane component PilP / Pilus assembly protein, PilP / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Type IV pilus inner membrane component PilP / PilP protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDerrick, J.P. / Berry, J.
CitationJournal: To be Published
Title: Structure of a Domain from the Type Iv Pilus Biogenesis Lipoprotein Pilp
Authors: Berry, J. / Derrick, J.P.
History
DepositionJan 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PILP PROTEIN
B: PILP PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,3072
Polymers20,3072
Non-polymers00
Water1,928107
1
A: PILP PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,1541
Polymers10,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PILP PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,1541
Polymers10,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.240, 87.790, 42.210
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.757, 0.04987, 0.6515), (-0.04201, -0.9987, 0.02764), (0.6521, -0.006444, 0.7581)
Vector: 26.76, -12.25, 3.887)

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Components

#1: Protein PILP PROTEIN / PILP / TYPE 4 FIMBRIAL BIOGENESIS PROTEIN PILP


Mass: 10153.529 Da / Num. of mol.: 2 / Fragment: RESIDUES 83-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q51354, UniProt: G3XCX7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGSHM SEQUENCE IS FROM THE EXPRESSION VECTOR (PET15B) AFTER THROMBIN CLEAVAGE

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 8% (V/V) ETHYLENE GLYCOL, 20% (W/V) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 16259 / % possible obs: 86.7 % / Observed criterion σ(I): 2.4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y4Y

2y4y


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.669 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.282 842 5.2 %RANDOM
Rwork0.23 ---
obs0.233 15372 85.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.35 Å2
2---0.31 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 0 107 1451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221364
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3211.9661837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9595173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24924.06264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211032
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9541.5853
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.83321369
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1073511
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9074.5468
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.56131364
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.933 64 -
Rwork0.892 1116 -
obs--83.39 %

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