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- PDB-5vaw: Fusion of Maltose-binding Protein and PilA from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 5vaw
TitleFusion of Maltose-binding Protein and PilA from Acinetobacter baumannii AB5075
ComponentsMaltose-binding periplasmic protein,Type IV pilin PilA
KeywordsCELL ADHESION / Type IV Pilin
Function / homology
Function and homology information


pilus / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...pilus / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / cell adhesion / DNA damage response / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
GLUTAMIC ACID / LYSINE / SERINE / Prepilin-type N-terminal cleavage/methylation domain-containing protein / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Acinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsPiepenbrink, K.H. / Sundberg, E.J.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: The structure of PilA fromAcinetobacter baumanniiAB5075 suggests a mechanism for functional specialization inAcinetobactertype IV pili.
Authors: Ronish, L.A. / Lillehoj, E. / Fields, J.K. / Sundberg, E.J. / Piepenbrink, K.H.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr2_symmetry / _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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Type IV pilin PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6756
Polymers54,1351
Non-polymers5415
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.557, 103.040, 56.195
Angle α, β, γ (deg.)90.000, 98.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Maltose-binding periplasmic protein,Type IV pilin PilA / Type IV pilin structural subunit


Mass: 54134.625 Da / Num. of mol.: 1
Mutation: D82A, K83A, D87A, K88A, E172A, N173A, K239A, K362A, D363A,I369A, P370A
Source method: isolated from a genetically manipulated source
Details: This polypeptide is a fusion of Maltose Binding Protein with the soluble portion of PilA from A. baumannii AB5075
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Acinetobacter baumannii (bacteria)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: D8A942, UniProt: A0A0D5YCX7, UniProt: P0AEX9*PLUS

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Non-polymers , 6 types, 302 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES/imidazole pH6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02M DL-alanine, 0.02M glycine, 0.02M DL-lysine HCl, 0.02M DL-serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.69→29.21 Å / Num. obs: 47148 / % possible obs: 95 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.035 / Rrim(I) all: 0.074 / Net I/σ(I): 11.1 / Num. measured all: 194591 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.722.51.71409116130.2771.2612.1360.563.3
9.1-29.214.40.02514403270.9990.0130.02850.197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å29.21 Å
Translation2 Å29.21 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XA2

4xa2


Resolution: 1.69→29.208 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 3821 4.26 %
Rwork0.2089 85932 -
obs0.2103 89753 91.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.21 Å2 / Biso mean: 42.3566 Å2 / Biso min: 21.08 Å2
Refinement stepCycle: final / Resolution: 1.69→29.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 36 297 3913
Biso mean--74.2 43.68 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043754
X-RAY DIFFRACTIONf_angle_d0.615138
X-RAY DIFFRACTIONf_chiral_restr0.043588
X-RAY DIFFRACTIONf_plane_restr0.004670
X-RAY DIFFRACTIONf_dihedral_angle_d5.7832984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6902-1.71160.4729760.44021691176748
1.7116-1.73410.3887960.41352115221161
1.7341-1.75790.4333970.39092405250268
1.7579-1.7830.39491210.37972707282878
1.783-1.80960.37521280.38012792292080
1.8096-1.83790.3661290.3722981311087
1.8379-1.8680.3711460.3483314346094
1.868-1.90020.35011500.34693366351698
1.9002-1.93480.38551500.31723407355798
1.9348-1.9720.28631550.28163439359498
1.972-2.01220.24591520.2773385353798
2.0122-2.0560.30421510.26583426357798
2.056-2.10380.30151530.26683401355498
2.1038-2.15640.27821560.25843436359298
2.1564-2.21470.27061540.23763422357698
2.2147-2.27980.22151530.23623427358099
2.2798-2.35330.26771520.2323402355497
2.3533-2.43740.29111520.22523426357899
2.4374-2.5350.24421500.22083331348197
2.535-2.65030.29541570.22513429358698
2.6503-2.78990.27891480.21313407355598
2.7899-2.96450.25061520.21783426357898
2.9645-3.19320.22391510.19963403355498
3.1932-3.5140.24181440.18263342348695
3.514-4.02140.19471510.15863381353297
4.0214-5.06220.17361480.13963305345395
5.0622-29.21220.18361490.15853366351597
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)
11.45191.33140.87663.54740.69922.37030.07540.96670.3935-0.2616-0.1419-0.2150.08570.72990.02320.29620.12510.06740.62630.1280.285410.444732.4159-34.0136
22.5184-0.6510.38892.6584-2.42663.31950.2738-0.1276-0.8442-0.1949-0.12170.30870.10750.1473-0.11890.23130.0035-0.04810.2030.02750.4622-2.3988.3381-12.9802
35.1541-1.27130.0982.9657-0.43022.49440.1549-0.0405-0.3469-0.1045-0.08910.1099-0.10260.0694-0.06240.2348-0.0295-0.01810.16990.00390.2349-3.606214.9032-11.0884
41.68180.02480.80091.6715-1.11492.20590.35470.8713-0.0835-0.709-0.29830.20960.40230.6525-0.03930.53970.24650.01720.6092-0.00790.13684.629721.5172-34.5066
52.4767-0.77920.66454.0438-1.35351.01020.1585-0.15880.0232-0.0404-0.09650.0524-0.1855-0.0363-0.02070.21880.00670.01580.2464-0.0190.1964-5.525426.7502-13.8785
64.03250.1303-0.28791.00160.12750.8579-0.0612-0.07510.7676-0.04470.01740.07440.00210.0140.03050.17420.00580.00080.2285-0.05090.567721.635848.8648-11.4869
72.06910.46311.4562.69421.00742.8009-0.20640.4062-0.20580.1899-0.0443-0.0102-0.2217-0.53060.23611.78630.05460.68820.95770.03220.93874.270232.018-11.1027
83.46022.3588-3.13021.6414-2.13562.84451.56410.3227-2.4984-0.33960.1287-0.43261.04240.3995-1.66560.7658-0.0670.21280.3959-0.08910.900833.29259.9174-13.5154
92-4.42212.00012.00011.99992-6.545-4.623916.02731.19161.0948-2.6827-10.63071.89585.48291.0393-0.407-0.10371.0016-0.35221.10349.769625.7894-24.6662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 105 )A1 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 153 )A106 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 245 )A154 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 314 )A246 - 314
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 1023 )A315 - 1023
6X-RAY DIFFRACTION6chain 'A' and (resid 1024 through 1151 )A1024 - 1151
7X-RAY DIFFRACTION7chain 'A' and (resid 1203 through 1203 )A1203
8X-RAY DIFFRACTION8chain 'A' and (resid 1204 through 1204 )A1204
9X-RAY DIFFRACTION9chain 'A' and (resid 1205 through 1205 )A1205

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