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- PDB-1rg0: Monoclinic crystal form of the truncated K122-4 pilin from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 1rg0
TitleMonoclinic crystal form of the truncated K122-4 pilin from Pseudomonas aeruginosa
ComponentsFimbrial protein
KeywordsCELL ADHESION / Type IV Pilin / Lectin / Adhesin / Pseudomonas
Function / homology
Function and homology information


glycosphingolipid binding / biological process involved in interaction with host / pilus / periplasmic space / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAudette, G.F. / Irvin, R.T. / Hazes, B.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystallographic Analysis of the Pseudomonas aeruginosa Strain K122-4 Monomeric Pilin Reveals a Conserved Receptor-Binding Architecture
Authors: Audette, G.F. / Irvin, R.T. / Hazes, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, crystallization and preliminary diffraction studies of the Pseudomonas aeruginosa strain K122-4 monomeric pilin
Authors: Audette, G.F. / Irvin, R.T. / Hazes, B.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Derived calculations / Category: struct_biol / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). FOR AN EXPLANATION OF THE BIOLOGICAL UNIT, PLEASE REFER TO THE FOLLOWING REFERENCES: Parge, H.E., Forest, K.T., Hickey, M.J., Christensen, D.A., Getzoff, E.D., Tainer, J.A.: Structure of the fibre-forming protein pilin at 2.6 A resolution. Nature 378 pp. 32 (1995). Keizer, D.W., Slupsky, C.M., Kalisiak, M., Campbell, A.P., Crump, M.P., Sastry, P.A., Hazes, B., Irvin, R.T., Sykes, B.D.: Structure of a Pilin Monomer from Pseudomonas Aeruginosa. Implications for the Assembly of Pili. J.Biol.Chem. 276 pp. 24186 (2001).
Remark 999SEQUENCE THE AUTHORS STATE THE PROTEIN SEQUENCE AT RESIDUE 36 IS IS PROBABLY A SEQUENCING ERROR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)25,6912
Polymers25,6912
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.301, 80.720, 39.127
Angle α, β, γ (deg.)90.00, 113.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 6 / Auth seq-ID: 32 - 142 / Label seq-ID: 8 - 118

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe type IV pilins are initially produced as integral inner membrane proteins that are subsequently assembled into a helical fiber. This entry contains the crystallographic asymmetric unit which consists of 2 chain(s). For an explanation of the biological unit, please refer to the following references: Parge, H.E., Forest, K.T., Hickey, M.J., Christensen, D.A., Getzoff, E.D., Tainer, J.A.: Structure of the Fibre-Forming Protein Pilin at 2.6 A Resolution. Nature 378 PP. 32 (1995). Keizer, D.W., Slupsky, C.M., Kalisiak, M., Campbell, A.P., Crump, M.P., Sastry, P.A., Hazes, B., Irvin, R.T., Sykes, B.D.: Structure of a Pillin Monomer from Pseudomonas aeruginosa. Implications for the Assembly of Pili. J. Biol. Chem. 276, PP 2418 (2001).

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Components

#1: Protein Fimbrial protein / Pilin / Strain K122-4


Mass: 12845.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K122-4 / Gene: PILA, FIMA / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): ER2507 / References: UniProt: P17838
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 4000, Potassium Phosphate Monobasic, Sodium Cacodylate, Tris HCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2003
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.51→40.49 Å / Num. obs: 25475 / % possible obs: 78.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.195 / Net I/σ(I): 9.3
Reflection shellResolution: 1.51→1.63 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.6 / Num. unique all: 2771 / Rsym value: 0.01068 / % possible all: 68

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Processing

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

1qve


Resolution: 1.8→40.49 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.062 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25428 661 4.1 %RANDOM
Rwork0.23583 ---
all0.23661 16158 --
obs0.23661 15497 83.2 %-
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: 12.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20.01 Å2
2--1.23 Å20 Å2
3----0.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 89 1879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211816
X-RAY DIFFRACTIONr_bond_other_d00.021620
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9592475
X-RAY DIFFRACTIONr_angle_other_deg3.91833801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9635250
X-RAY DIFFRACTIONr_chiral_restr0.0580.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined0.250.2425
X-RAY DIFFRACTIONr_nbd_other0.3020.21825
X-RAY DIFFRACTIONr_nbtor_other0.1220.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.213
X-RAY DIFFRACTIONr_mcbond_it5.9251.51250
X-RAY DIFFRACTIONr_mcangle_it7.93522007
X-RAY DIFFRACTIONr_scbond_it8.4973566
X-RAY DIFFRACTIONr_scangle_it11.014.5468
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1480 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.445
loose thermal4.7610
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.299 48
Rwork0.311 1033
obs-1033
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)
15.7058-3.9997-5.60882.54363.79165.87810.09750.1272-0.0475-0.1384-0.10880.1092-0.2193-0.07130.01130.1298-0.00090.02140.0732-0.01160.048810.65154.70341.2664
20.3416-0.86620.36273.33570.97150.95170.0865-0.06220.11740.04410.115-0.2105-0.1388-0.0896-0.20150.0605-0.00130.01360.1621-0.04430.058623.6881-2.24313.2204
30.829-0.2694-0.41990.38090.68141.8540.00410.0160.04260.00980.0271-0.0074-0.02430.0469-0.03120.10120.00060.01390.0962-0.00330.011510.5354-1.033
44.7485-3.0332-0.88055.2391.90221.31480.1040.04450.1341-0.0006-0.11920.1794-0.1169-0.05760.01520.0749-0.02780.00220.0854-0.01670.0383-1.2790.69294.0979
5-1.0709-0.56821.04432.75682.60693.5163-0.0483-0.4430.0984-0.3876-0.27290.2361-0.0215-0.14910.32120.03220.00510.02880.1256-0.03870.1387-10.8569-9.5497-1.2634
63.76950.78895.15910.83380.46466.78820.0945-0.0779-0.0669-0.0792-0.03910.02580.3025-0.0631-0.05550.1347-0.01230.0190.0896-0.0040.035312.08818.634128.5996
72.20530.1455-0.50080.22122.6209-0.5413-0.04710.1840.05670.07150.0167-0.1583-0.07250.0750.03040.06580.00270.00940.15290.03670.051925.010125.89929.8011
80.6630.01461.03310.5545-0.26953.63120.05730.0089-0.1432-0.04080.06320.00070.120.0277-0.12050.0855-0.00140.01370.09860.00640.042311.834824.374529.3113
96.00750.02542.67091.0625-0.18275.3802-0.00580.0367-0.3705-0.03490.06070.30470.1497-0.2505-0.05480.09520.00450.01270.112-0.00560.06810.089123.921827.4947
1010.9039-6.7825-4.89226.18312.23163.3494-0.13960.349-0.11940.3311-0.04510.09790.0458-0.15190.18480.0533-0.0172-0.00180.1125-0.00690.0157-8.471329.095436.0787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 541 - 30
2X-RAY DIFFRACTION2AA55 - 7231 - 48
3X-RAY DIFFRACTION3AA73 - 12849 - 104
4X-RAY DIFFRACTION4AA129 - 142105 - 118
5X-RAY DIFFRACTION5AA143 - 150119 - 126
6X-RAY DIFFRACTION6BB25 - 541 - 30
7X-RAY DIFFRACTION7BB55 - 7231 - 48
8X-RAY DIFFRACTION8BB73 - 12849 - 104
9X-RAY DIFFRACTION9BB129 - 142105 - 118
10X-RAY DIFFRACTION10BB143 - 149119 - 125

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