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- PDB-1x6r: Structure 5: room temperature crystal structure of the truncated ... -

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Basic information

Entry
Database: PDB / ID: 1x6r
TitleStructure 5: room temperature crystal structure of the truncated pak pilin from Pseudomonas aeruginosa at 1.80A resolution
ComponentsFimbrial protein
KeywordsSTRUCTURAL PROTEIN / TYPE IV PILIN / LECTIN / ADHESIN
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / cell adhesion / membrane
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsDunlop, K.V. / Irvin, R.T. / Hazes, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
Authors: Dunlop, K.V. / Irvin, R.T. / Hazes, B.
History
DepositionAug 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)12,6961
Polymers12,6961
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.042, 38.042, 149.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsProtein assembles to form a fiber. See PDB codes 1DZO and 1AY2

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Components

#1: Protein Fimbrial protein / Pilin / Strain PAK


Mass: 12696.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K / Cellular location: EXTRACELLULAR FILAMENTOUS APPENDAGE / Gene: pilA, fimA / Plasmid: PRLD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: 60% Ammonium Sulfate, 0.1M Hepes, pH 8.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 10, 2001 / Details: SUPPER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→23.6 Å / Num. all: 10367 / Num. obs: 10367 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.59
Reflection shellResolution: 1.8→1.85 Å / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZO

1dzo


Resolution: 1.82→23.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.192 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17744 523 5 %RANDOM
Rwork0.14981 ---
all0.15115 10367 --
obs0.15115 10367 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.82→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 0 82 935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021888
X-RAY DIFFRACTIONr_bond_other_d0.0020.02822
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9721206
X-RAY DIFFRACTIONr_angle_other_deg1.00231932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02150
X-RAY DIFFRACTIONr_nbd_refined0.2160.2142
X-RAY DIFFRACTIONr_nbd_other0.2480.2891
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4530.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.29
X-RAY DIFFRACTIONr_symmetry_hbond_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: 1.82→1.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 38
Rwork0.231 531
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2333-1.2009-1.89181.79892.66353.85270.032-0.0141-0.0490.0608-0.04730.0396-0.02550.03060.01530.07260.015-0.00130.051-0.00130.05077.61435.049247.8119
21.8-0.0815-0.5910.26341.1090.4396-0.03990.1837-0.00930.00790.06270.0586-0.05460.0381-0.02270.06120.0147-0.00660.07190.00540.05764.75721.541631.7954
30.31-0.1243-0.5970.60380.33570.7127-0.03160.04730.05190.04550.0221-0.0309-0.00260.01780.00950.04680.0322-0.01040.0639-0.01020.048411.367511.47644.1804
44.8428-1.5601-2.02261.4258-3.03360.4968-0.3001-0.3360.11540.17820.145-0.1591-0.10620.0940.15510.12030.0319-0.05250.086-0.03980.034214.02213.697957.767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 54
2X-RAY DIFFRACTION2A55 - 79
3X-RAY DIFFRACTION3A80 - 133
4X-RAY DIFFRACTION4A134 - 144

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