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- PDB-5irb: Structural insight into host cell surface retention of a 1.5-MDa ... -

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Basic information

Entry
Database: PDB / ID: 5irb
TitleStructural insight into host cell surface retention of a 1.5-MDa bacterial ice-binding adhesin
ComponentsRTX-adhesin
KeywordsCELL ADHESION / Ice-binding protein / Biofilm-associated protein / RTX-adhesin
Function / homologyImmunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Antifreeze protein
Function and homology information
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuo, S. / Phippen, S. / Campbell, R. / Davies, P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Adv / Year: 2017
Title: Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.
Authors: Guo, S. / Stevens, C.A. / Vance, T.D.R. / Olijve, L.L.C. / Graham, L.A. / Campbell, R.L. / Yazdi, S.R. / Escobedo, C. / Bar-Dolev, M. / Yashunsky, V. / Braslavsky, I. / Langelaan, D.N. / ...Authors: Guo, S. / Stevens, C.A. / Vance, T.D.R. / Olijve, L.L.C. / Graham, L.A. / Campbell, R.L. / Yazdi, S.R. / Escobedo, C. / Bar-Dolev, M. / Yashunsky, V. / Braslavsky, I. / Langelaan, D.N. / Smith, S.P. / Allingham, J.S. / Voets, I.K. / Davies, P.L.
History
DepositionMar 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RTX-adhesin
B: RTX-adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,17022
Polymers64,3782
Non-polymers79220
Water10,359575
1
A: RTX-adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,59011
Polymers32,1891
Non-polymers40110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RTX-adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,58011
Polymers32,1891
Non-polymers39110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-198 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.601, 247.023, 84.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RTX-adhesin


Mass: 32189.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct was cloned into the NdeI and XhoI sites of the pET24a vector. Therefore at the protein's C terminus, two extra aminoacids (LE; XhoI) were present before the His-Tag.
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5 / Details: PEG3350, calcium chloride

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.8→123.51 Å / Num. obs: 60756 / % possible obs: 99.5 % / Redundancy: 8.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.03 Å / CC1/2: 0.467 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.789 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2974 4.91 %RANDOM
Rwork0.2095 ---
obs0.2111 60518 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 23 575 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094430
X-RAY DIFFRACTIONf_angle_d1.256096
X-RAY DIFFRACTIONf_dihedral_angle_d12.3491451
X-RAY DIFFRACTIONf_chiral_restr0.054803
X-RAY DIFFRACTIONf_plane_restr0.006804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.37561250.33412732X-RAY DIFFRACTION99
2.0328-2.06780.37151360.31982680X-RAY DIFFRACTION99
2.0678-2.10540.33111500.31182699X-RAY DIFFRACTION99
2.1054-2.14590.31571260.29182714X-RAY DIFFRACTION99
2.1459-2.18970.32941540.27332683X-RAY DIFFRACTION99
2.1897-2.23740.28381240.26742669X-RAY DIFFRACTION99
2.2374-2.28940.30741570.25932739X-RAY DIFFRACTION100
2.2894-2.34660.26131380.2452706X-RAY DIFFRACTION100
2.3466-2.41010.24911410.23822716X-RAY DIFFRACTION100
2.4101-2.4810.28571420.23612710X-RAY DIFFRACTION100
2.481-2.56110.23481320.22342753X-RAY DIFFRACTION100
2.5611-2.65260.251540.21692699X-RAY DIFFRACTION100
2.6526-2.75880.22481290.2162747X-RAY DIFFRACTION100
2.7588-2.88430.29881150.22412769X-RAY DIFFRACTION100
2.8843-3.03630.28751370.23842754X-RAY DIFFRACTION100
3.0363-3.22650.22621580.19612731X-RAY DIFFRACTION100
3.2265-3.47550.25271370.19762762X-RAY DIFFRACTION100
3.4755-3.82510.20791420.19692773X-RAY DIFFRACTION100
3.8251-4.37810.22551580.17182774X-RAY DIFFRACTION100
4.3781-5.51410.18221490.15132813X-RAY DIFFRACTION100
5.5141-42.79910.1741700.16672921X-RAY DIFFRACTION100
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)
11.23190.20460.34367.2403-0.07551.1240.2008-0.07940.0964-0.1295-0.16040.27880.1997-0.1765-0.04040.4878-0.0174-0.03120.24640.01750.1933-27.88462.0352-9.8866
24.21266.6915-0.237224.275-1.33083.562-0.0542-0.2499-0.3760.2384-0.1527-0.7743-0.17240.0830.20690.1410.00860.03060.19570.00950.4212-28.196-37.6998-3.9117
32.7903-0.4089-0.306710.09060.59682.23750.1438-0.1501-0.44450.1098-0.20250.01430.3108-0.08120.05870.13130.00630.01220.09370.01290.5047-35.9326-57.1562-1.9134
41.52890.98440.33946.44960.43711.5993-0.0195-0.0125-0.0657-0.3843-0.16990.4805-0.004-0.15320.18940.13080.0143-0.01060.1499-0.02590.496-38.7438-43.8391-4.1684
511.5195-3.29386.472710.89888.284515.96990.14030.4-0.0287-1.89930.0936-0.5821-0.41630.201-0.23391.327-0.19380.31840.047-0.07760.43-34.5082-52.6874-13.1832
60.80731.1540.605112.64710.80981.1922-0.13590.0516-0.1081-0.80330.07110.0076-0.1320.09280.06470.16740.01680.02240.09450.00210.3891-33.0761-41.7854-8.0997
72.93520.9596-0.58864.55420.79921.9563-0.0048-0.2844-0.68760.445-0.1917-0.04770.1896-0.04160.19640.15930.00580.01750.15780.03940.7622-30.8466-94.99910.8728
82.88391.2933-0.08793.83240.74451.70630.0036-0.2794-0.58920.4311-0.2080.1590.1444-0.1940.20440.1524-0.01080.05550.17370.02030.7199-34.5356-92.19121.8868
91.2177-0.5439-0.18373.2829-1.37041.4440.14990.0630.252-0.4435-0.06130.0233-0.73760.0495-0.08861.1802-0.02250.00990.1248-0.03530.2149-58.89031.869411.0302
100.7534-1.3010.01315.5068-1.04940.65090.2620.1371-0.1956-0.8128-0.33250.3923-0.3636-0.04020.07050.91710.0862-0.10950.1745-0.06940.3523-60.8818-22.90516.5323
111.99120.7478-0.35519.20520.05051.49910.1530.0512-0.17730.0662-0.1797-0.46180.09940.01120.02670.1118-0.03210.00970.1804-0.03550.5025-51.4712-56.98243.5499
121.3224-0.13330.18755.91990.04970.67690.1473-0.0343-0.02670.4659-0.2124-0.4615-0.02940.07820.06520.1581-0.0331-0.00280.1429-0.02750.5471-49.3675-44.18287.2321
130.83971.5935-0.307629.9668-4.84273.08740.36-0.16640.04841.8944-0.48320.2219-0.10630.02490.12330.2358-0.07240.00180.1673-0.05440.391-53.5182-45.814713.3875
140.09180.29750.041912.73331.02460.63090.101-0.073-0.01890.9661-0.14110.081-0.0071-0.17550.04010.1761-0.05790.05020.1096-0.05920.4408-56.3209-45.492110.483
150.9760.19310.23016.0831-0.15640.76010.06270.0878-0.0666-0.521-0.0838-0.78920.07640.08290.0210.1206-0.01350.09170.0968-0.00980.5028-55.0132-92.1916-4.108
1617.2705-6.97983.207536.32193.670124.8509-0.15941.3315-1.0317-1.06340.6896-0.11232.1541.2474-0.53030.2770.03790.04010.21230.03640.6489-49.5868-111.4193-4.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 182:290 )A182 - 290
2X-RAY DIFFRACTION2( CHAIN A AND RESID 291:297 )A291 - 297
3X-RAY DIFFRACTION3( CHAIN A AND RESID 298:320 )A298 - 320
4X-RAY DIFFRACTION4( CHAIN A AND RESID 321:360 )A321 - 360
5X-RAY DIFFRACTION5( CHAIN A AND RESID 361:366 )A361 - 366
6X-RAY DIFFRACTION6( CHAIN A AND RESID 367:392 )A367 - 392
7X-RAY DIFFRACTION7( CHAIN A AND RESID 393:438 )A393 - 438
8X-RAY DIFFRACTION8( CHAIN A AND RESID 439:494 )A439 - 494
9X-RAY DIFFRACTION9( CHAIN B AND RESID 183:275 )B183 - 275
10X-RAY DIFFRACTION10( CHAIN B AND RESID 276:302 )B276 - 302
11X-RAY DIFFRACTION11( CHAIN B AND RESID 303:320 )B303 - 320
12X-RAY DIFFRACTION12( CHAIN B AND RESID 321:360 )B321 - 360
13X-RAY DIFFRACTION13( CHAIN B AND RESID 361:372 )B361 - 372
14X-RAY DIFFRACTION14( CHAIN B AND RESID 373:393 )B373 - 393
15X-RAY DIFFRACTION15( CHAIN B AND RESID 394:490 )B394 - 490
16X-RAY DIFFRACTION16( CHAIN B AND RESID 491:496 )B491 - 496

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