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- PDB-1x6p: Structure 4; room temperature crystal structure of truncated pak ... -

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Basic information

Entry
Database: PDB / ID: 1x6p
TitleStructure 4; room temperature crystal structure of truncated pak pilin from Pseudomonas aeruginosa at 1.63A 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: 1.63 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 1.4Oct 30, 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
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.114, 38.114, 149.775
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.: 138 / 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: 42.2 %
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: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: SUPPER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→37.53 Å / Num. all: 14500 / Num. obs: 14500 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.62 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 26.7
Reflection shellResolution: 1.63→1.72 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 10.1 / Rsym value: 0.19 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZO

1dzo


Resolution: 1.63→37.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15765 751 5.2 %RANDOM
Rwork0.13965 ---
all0.14056 14500 --
obs0.14056 14500 99.5 %-
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: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 138 984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021877
X-RAY DIFFRACTIONr_bond_other_d0.0010.02804
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9691194
X-RAY DIFFRACTIONr_angle_other_deg1.23931884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.483119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68615160
X-RAY DIFFRACTIONr_chiral_restr0.0890.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02150
X-RAY DIFFRACTIONr_nbd_refined0.2170.3161
X-RAY DIFFRACTIONr_nbd_other0.1950.3719
X-RAY DIFFRACTIONr_nbtor_other0.0160.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.596
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.5030.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.514
LS refinement shellResolution: 1.633→1.676 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.205 42
Rwork0.202 927
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)
10.6404-0.654-1.0611.07441.67282.29090.0194-0.0014-0.05140.0209-0.03210.0381-0.02580.03560.01270.06850.01550.00270.0459-0.00520.03747.65464.945847.6741
21.7248-0.2702-0.49960.3731.00210.4223-0.05170.14670.0130.06360.07270.0188-0.0170.0185-0.0210.04870.0103-0.00560.0587-0.00080.04464.74621.528731.9254
30.0807-0.0736-0.33320.34330.13480.2328-0.03380.03360.03010.04860.0193-0.0206-0.01830.02810.01450.05190.0249-0.00790.0652-0.01290.044211.419511.456244.1814
44.4508-1.1605-1.0161.8514-1.3927-0.6751-0.1501-0.1770.07520.2280.0297-0.0852-0.0098-0.00010.12040.09640.0237-0.02890.0629-0.01450.009614.005213.730857.8546
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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