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- PDB-6mlt: Crystal structure of the V. cholerae biofilm matrix protein Bap1 -

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Basic information

Entry
Database: PDB / ID: 6mlt
TitleCrystal structure of the V. cholerae biofilm matrix protein Bap1
ComponentsHemolysin-related protein
KeywordsSUGAR BINDING PROTEIN / biofilm matrix protein / carbohydrate-binding protein / metal-binding protein / secreted protein
Function / homologyHemolysin, beta-prism lectin / Beta-prism lectin / Jacalin-like lectin domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / CITRATE ANION / Hemolysin-related protein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsKaus, K. / Biester, A. / Chupp, E. / Lu, K. / Vidsudharomn, C. / Olson, R.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The 1.9 angstrom crystal structure of the extracellular matrix protein Bap1 fromVibrio choleraeprovides insights into bacterial biofilm adhesion.
Authors: Kaus, K. / Biester, A. / Chupp, E. / Lu, J. / Visudharomn, C. / Olson, R.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,80611
Polymers66,2381
Non-polymers56810
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.951, 70.951, 303.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemolysin-related protein


Mass: 66237.812 Da / Num. of mol.: 1 / Mutation: Y415-K471 Deletion
Source method: isolated from a genetically manipulated source
Details: Loop including residues Y415-K471 deleted genetically
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1888 / Plasmid: pNGFP-BC / Details (production host): N-terminal GFP fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): NEB T7 Express / References: UniProt: Q9KQW0

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Non-polymers , 5 types, 481 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium citrate, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.25414 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25414 Å / Relative weight: 1
ReflectionResolution: 1.9→47.64 Å / Num. obs: 62568 / % possible obs: 99.7 % / Redundancy: 11.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.12 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.943.80.63937720.6620.3560.73896.2
9.11-47.6411.20.077100.9970.0210.07399.2

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS20170615data reduction
Aimless0.5.32data scaling
AutoSol1.11.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→47.64 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 15.76
RfactorNum. reflection% reflection
Rfree0.1762 3191 5.11 %
Rwork0.161 --
obs0.1617 62422 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.95 Å2 / Biso mean: 30.2647 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: final / Resolution: 1.9→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 53 471 5047
Biso mean--42.85 35.3 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044644
X-RAY DIFFRACTIONf_angle_d0.6416341
X-RAY DIFFRACTIONf_chiral_restr0.054705
X-RAY DIFFRACTIONf_plane_restr0.004834
X-RAY DIFFRACTIONf_dihedral_angle_d9.7282679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.92840.34541440.3597239394
1.9284-1.95860.3691370.30182491100
1.9586-1.99070.27861320.26462507100
1.9907-2.0250.2031310.21822570100
2.025-2.06180.2011440.17672507100
2.0618-2.10150.21381210.17242559100
2.1015-2.14440.18771160.17752577100
2.1444-2.1910.19291570.17172495100
2.191-2.2420.17051440.16432533100
2.242-2.2980.17831260.15412585100
2.298-2.36020.19481390.14932542100
2.3602-2.42960.16061350.14362536100
2.4296-2.5080.15441500.14442566100
2.508-2.59770.19661170.14952584100
2.5977-2.70170.17611560.14822554100
2.7017-2.82460.1771330.15652579100
2.8246-2.97350.16961330.15732608100
2.9735-3.15980.17631570.15362561100
3.1598-3.40370.14691420.14832620100
3.4037-3.74610.15961130.14162662100
3.7461-4.28780.13491450.12572642100
4.2878-5.4010.13721750.12932667100
5.401-47.640.21651440.20052893100
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)
10.58410.04340.14630.7823-0.30510.7345-0.01860.00660.0058-0.03560.00590.0534-0.0368-0.08540.02130.15440.01570.00920.1787-0.02520.15727.699530.259995.9223
21.2089-1.0078-1.13290.83940.9471.1061-0.06530.0273-0.12980.1206-0.05050.1180.07960.05020.11390.3007-0.01260.02830.1914-0.03430.22256.407839.3697134.1531
31.7217-0.7924-0.13561.89980.18842.32170.0125-0.02540.0341-0.04620.0269-0.1230.26320.1503-0.04040.2541-0.00580.03630.1515-0.02320.19152.974648.759142.8326
40.33410.0063-0.30370.1055-0.00480.2743-0.0485-0.1686-0.03590.10880.00360.041-0.12320.1335-0.00430.2280.017-0.00680.21890.00140.17531.74531.3696122.4792
50.91530.1237-0.01920.7329-0.10941.1563-0.0009-0.0769-0.09960.0399-0.00990.02310.0591-0.05310.01280.16680.00270.01480.1745-0.00420.186628.897619.5314106.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 298 )A31 - 298
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 363 )A299 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 505 )A364 - 505
4X-RAY DIFFRACTION4chain 'A' and (resid 506 through 545 )A506 - 545
5X-RAY DIFFRACTION5chain 'A' and (resid 546 through 690 )A546 - 690

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