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- PDB-3hx6: Crystal structure of Pseudomonas aeruginosa PilY1 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3hx6
TitleCrystal structure of Pseudomonas aeruginosa PilY1 C-terminal domain
ComponentsType 4 fimbrial biogenesis protein PilY1
KeywordsCELL ADHESION / beta propeller / pilus protein
Function / homologyPilC beta-propeller domain / Neisseria PilC beta-propeller domain / type IV pilus-dependent motility / pilus / Quinoprotein alcohol dehydrogenase-like superfamily / calcium ion binding / membrane / cytosol / Type IV pilus biogenesis factor PilY1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRedinbo, M.R. / Orans, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility.
Authors: Orans, J. / Johnson, M.D. / Coggan, K.A. / Sperlazza, J.R. / Heiniger, R.W. / Wolfgang, M.C. / Redinbo, M.R.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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: Type 4 fimbrial biogenesis protein PilY1
B: Type 4 fimbrial biogenesis protein PilY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9004
Polymers122,8202
Non-polymers802
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Type 4 fimbrial biogenesis protein PilY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4502
Polymers61,4101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Type 4 fimbrial biogenesis protein PilY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4502
Polymers61,4101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 108.000, 159.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type 4 fimbrial biogenesis protein PilY1


Mass: 61409.883 Da / Num. of mol.: 2 / Fragment: C-terminal domain: UNP residues 613-1161 / Mutation: L705M, L805M, L816M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pilY1, PA4554 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): PAK / References: UniProt: Q9HVM8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.02 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.3 M Sodium malonate pH 6.5, 20% PEG 3350, 50 mM DTT, 30-100 mM (NH4)3PO4, 4-8% Trifluoroethanol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 10, 2007
MARMOSAIC 225 mm CCD2CCDOct 10, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MirrorsSINGLE WAVELENGTHMx-ray1
2MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
211
ReflectionResolution: 2.1→50 Å / Num. all: 118348 / Num. obs: 118348 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflectionSelection details
Rfree0.2353 3273 Random
Rwork0.196 --
all0.213 118348 -
obs0.213 118348 -
Solvent computationBsol: 42.2522 Å2 / ksol: 0.358053 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2---2.633 Å20 Å2
3---0.333 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7363 0 2 760 8125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005299
X-RAY DIFFRACTIONc_angle_deg1.36784
X-RAY DIFFRACTIONc_mcbond_it1.4651.5
X-RAY DIFFRACTIONc_mcangle_it2.3992
X-RAY DIFFRACTIONc_scbond_it2.0722
X-RAY DIFFRACTIONc_scangle_it32.5

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