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- PDB-6p5t: Surface-layer (S-layer) RsaA protein from Caulobacter crescentus ... -

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Basic information

Entry
Database: PDB / ID: 6p5t
TitleSurface-layer (S-layer) RsaA protein from Caulobacter crescentus bound to strontium and iodide
ComponentsS-layer protein
KeywordsMEMBRANE PROTEIN / surface array / self-assembling / coat protein / RTX motif
Function / homology
Function and homology information


S-layer / calcium ion binding / extracellular region
Similarity search - Function
RsaA N-terminal domain / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
IODIDE ION / STRONTIUM ION / S-layer protein
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChan, A.C. / Herrmann, J. / Smit, J. / Wakatsuki, S. / Murphy, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-04802 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly.
Authors: Herrmann, J. / Li, P.N. / Jabbarpour, F. / Chan, A.C.K. / Rajkovic, I. / Matsui, T. / Shapiro, L. / Smit, J. / Weiss, T.M. / Murphy, M.E.P. / Wakatsuki, S.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
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.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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein
B: S-layer protein
C: S-layer protein
D: S-layer protein
E: S-layer protein
F: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,318280
Polymers460,4176
Non-polymers29,900274
Water87,1394837
1
B: S-layer protein
D: S-layer protein
E: S-layer protein
hetero molecules

A: S-layer protein
C: S-layer protein
F: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,318280
Polymers460,4176
Non-polymers29,900274
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y+1/2,-z+21
Unit cell
Length a, b, c (Å)210.729, 80.564, 221.833
Angle α, β, γ (deg.)90.000, 117.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 251 through 287 or resid 289...
21(chain B and (resid 251 through 287 or resid 289...
31(chain C and (resid 251 through 287 or resid 289...
41(chain D and (resid 251 through 287 or resid 289...
51(chain E and (resid 251 through 287 or resid 289...
61(chain F and (resid 251 through 287 or resid 289...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 251 through 287 or resid 289...AA251 - 28739 - 75
12GLYGLYILEILE(chain A and (resid 251 through 287 or resid 289...AA289 - 31377 - 101
13GLYGLYSERSER(chain A and (resid 251 through 287 or resid 289...AA315 - 452103 - 240
14THRTHRALAALA(chain A and (resid 251 through 287 or resid 289...AA454 - 1026242 - 814
21THRTHRLEULEU(chain B and (resid 251 through 287 or resid 289...BB251 - 28739 - 75
22GLYGLYILEILE(chain B and (resid 251 through 287 or resid 289...BB289 - 31377 - 101
23GLYGLYSERSER(chain B and (resid 251 through 287 or resid 289...BB315 - 452103 - 240
24THRTHRALAALA(chain B and (resid 251 through 287 or resid 289...BB454 - 1026242 - 814
31THRTHRLEULEU(chain C and (resid 251 through 287 or resid 289...CC251 - 28739 - 75
32GLYGLYILEILE(chain C and (resid 251 through 287 or resid 289...CC289 - 31377 - 101
33GLYGLYSERSER(chain C and (resid 251 through 287 or resid 289...CC315 - 452103 - 240
34THRTHRALAALA(chain C and (resid 251 through 287 or resid 289...CC454 - 1026242 - 814
41THRTHRLEULEU(chain D and (resid 251 through 287 or resid 289...DD251 - 28739 - 75
42GLYGLYILEILE(chain D and (resid 251 through 287 or resid 289...DD289 - 31377 - 101
43GLYGLYSERSER(chain D and (resid 251 through 287 or resid 289...DD315 - 452103 - 240
44THRTHRALAALA(chain D and (resid 251 through 287 or resid 289...DD454 - 1026242 - 814
51THRTHRLEULEU(chain E and (resid 251 through 287 or resid 289...EE251 - 28739 - 75
52GLYGLYILEILE(chain E and (resid 251 through 287 or resid 289...EE289 - 31377 - 101
53GLYGLYSERSER(chain E and (resid 251 through 287 or resid 289...EE315 - 452103 - 240
54THRTHRALAALA(chain E and (resid 251 through 287 or resid 289...EE454 - 1026242 - 814
61THRTHRLEULEU(chain F and (resid 251 through 287 or resid 289...FF251 - 28739 - 75
62GLYGLYILEILE(chain F and (resid 251 through 287 or resid 289...FF289 - 31377 - 101
63GLYGLYSERSER(chain F and (resid 251 through 287 or resid 289...FF315 - 452103 - 240
64THRTHRALAALA(chain F and (resid 251 through 287 or resid 289...FF454 - 1026242 - 814

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Components

#1: Protein
S-layer protein / / Paracrystalline surface layer protein


Mass: 76736.203 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: rsaA, CC_1007 / Production host: Escherichia coli (E. coli) / References: UniProt: P35828
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 150 / Source method: obtained synthetically / Formula: I
#3: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4837 / 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: 3.63 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 8.5% PEG 8000, 100 mM Tris-HCl, 150 mM strontium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.3 Å / Num. obs: 384732 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.1 / Rrim(I) all: 0.25 / Net I/σ(I): 8.1 / Num. measured all: 2446368 / Scaling rejects: 1483
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.145.51.834100730183720.6180.8392.0251.396.8
11.5-49.35.80.0571450624920.9970.0250.06229.898.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8P

5n8p


Resolution: 2.1→49.3 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.67
RfactorNum. reflection% reflection
Rfree0.2427 19202 5 %
Rwork0.2055 --
obs0.2074 384015 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 38.5156 Å2 / Biso min: 3.09 Å2
Refinement stepCycle: final / Resolution: 2.1→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30881 0 274 4839 35994
Biso mean--48.25 35.49 -
Num. residues----4682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13860X-RAY DIFFRACTION6.097TORSIONAL
12B13860X-RAY DIFFRACTION6.097TORSIONAL
13C13860X-RAY DIFFRACTION6.097TORSIONAL
14D13860X-RAY DIFFRACTION6.097TORSIONAL
15E13860X-RAY DIFFRACTION6.097TORSIONAL
16F13860X-RAY DIFFRACTION6.097TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.3766140.3449117011231595
2.1239-2.14880.33886280.3261119181254699
2.1488-2.17510.35036400.31981215912799100
2.1751-2.20260.33136330.30561194912582100
2.2026-2.23160.3236410.2931222912870100
2.2316-2.26210.30166410.2791201312654100
2.2621-2.29450.31346340.28011219212826100
2.2945-2.32870.30676380.26731203212670100
2.3287-2.36510.28256460.26141223112877100
2.3651-2.40390.28246250.25151201312638100
2.4039-2.44530.31756430.251222512868100
2.4453-2.48980.31246480.24821207112719100
2.4898-2.53770.2756330.23741217512808100
2.5377-2.58950.2916330.23741213912772100
2.5895-2.64580.28016390.23271210412743100
2.6458-2.70730.28166480.22561218612834100
2.7073-2.7750.28186390.22051218012819100
2.775-2.850.26716330.2161210512738100
2.85-2.93390.25186320.20871213912771100
2.9339-3.02860.24486490.20711217212821100
3.0286-3.13680.24936410.20841218912830100
3.1368-3.26240.23246420.19371221912861100
3.2624-3.41080.21016410.18111220612847100
3.4108-3.59060.21596440.17291218512829100
3.5906-3.81550.19186430.16821227712920100
3.8155-4.10990.19976470.1681222212869100
4.1099-4.52330.18736440.14581229012934100
4.5233-5.17720.17446430.13891225112894100
5.1772-6.52030.2116530.17441239913052100
6.5203-49.31690.20326670.1831264213309100
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)
10.0033-0.0058-0.00330.0060.00470.002-0.038-0.02350.02240.0163-0.02210.03960.0403-0.0478-00.24830.00520.00450.1126-0.00720.2727120.289121.5863185.9875
20.0855-0.01860.06070.10.05570.04370.01250.0837-0.00590.0348-0.00030.08590.0350.14920.01750.197-0.03830.03040.00160.07010.2723144.03271.2883184.7985
30.0423-0.01930.0122-0.01380.01090.03060.03340.08430.0317-0.01-0.05140.021-0.04090.1989-00.1795-0.0342-0.00270.2950.01060.2561186.1016-9.848191.7912
40.07510.050.06090.03460.01070.06940.0083-0.12450.03940.01560.0172-0.0103-0.06020.044200.2108-0.01770.00280.40220.01120.2336189.9658-16.7599240.7558
50.00020.00210.00030.0053-0.00050.00090.0540.01590.0025-0.015-0.02210.02590.0217-0.095800.2020.0038-0.01560.1346-0.01350.2369131.572558.308186.3368
60.0884-0.0239-0.02520.01470.030.10920.0353-0.0029-0.0569-0.0150.0080.1091-0.00760.14760.01350.1710.00230.00120.10430.0060.2378152.150139.7085187.9184
70.0502-0.04130.00530.050.02030.01180.04330.0734-0.0591-0.0169-0.00980.0191-0.01590.169200.18390.0315-0.0090.3249-0.04930.2639191.587630.5502189.7038
80.0309-0.01190.04630.03850.07780.0915-0.0323-0.0692-0.0450.0548-0.03740.01430.0332-0.073100.26480.01880.03880.5713-0.01320.2714201.413923.2042240.682
90.28710.10060.15320.23710.09170.12170.04320.46440.0030.05-0.08960.02120.0264-0.0056-0.05280.16360.1097-0.01120.4845-0.05660.2218114.82882.4794144.4733
100.08070.0433-0.080.2088-0.04230.07210.02370.1665-0.14310.1505-0.1443-0.1792-0.121-0.1787-0.10330.25030.00150.09531.0601-0.22060.2465171.1522-16.2186129.557
110.2346-0.06560.07410.21320.07860.15810.02760.40910.01770.0695-0.07220.08990.031-0.0411-0.00150.14150.008-0.05050.4319-0.05590.1364126.602439.203145.257
120.079-0-0.02290.06580.1130.05790.0320.1374-0.01470.0349-0.0419-0.07630.011-0.1086-0.00180.2344-0.0013-0.00010.8062-0.00080.3372183.657521.2252133.0328
130.0540.11770.02940.106-0.02180.16160.0030.04780.0121-0.0174-0.0306-0.04510.0009-0.1787-0.00010.22490.014-0.02130.3334-0.02580.216976.636545.4275157.658
140.09690.1079-0.04590.0982-0.08270.1-0.1276-0.0024-0.0329-0.0179-0.0406-0.0614-0.00930.0601-0.04070.281-0.01330.01890.65830.07860.231694.066727.100598.7126
150.05690.11790.02240.04160.00060.1910.06910.0788-0.02810.01480.007-0.0480.0582-0.01580.02990.18780.0532-0.02320.2215-0.04860.178865.65484.5222154.4361
160.09920.1263-0.10210.1011-0.1570.1428-0.2117-0.0529-0.015-0.02860.0585-0.06350.04370.0711-0.00450.30630.01340.04840.5914-0.02590.231685.2487-14.208795.9088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 245 through 285 )A245 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 539 )A286 - 539
3X-RAY DIFFRACTION3chain 'A' and (resid 540 through 749 )A540 - 749
4X-RAY DIFFRACTION4chain 'A' and (resid 750 through 1026 )A750 - 1026
5X-RAY DIFFRACTION5chain 'B' and (resid 251 through 300 )B251 - 300
6X-RAY DIFFRACTION6chain 'B' and (resid 301 through 496 )B301 - 496
7X-RAY DIFFRACTION7chain 'B' and (resid 497 through 728 )B497 - 728
8X-RAY DIFFRACTION8chain 'B' and (resid 729 through 1026 )B729 - 1026
9X-RAY DIFFRACTION9chain 'C' and (resid 247 through 660 )C247 - 660
10X-RAY DIFFRACTION10chain 'C' and (resid 661 through 1026 )C661 - 1026
11X-RAY DIFFRACTION11chain 'D' and (resid 247 through 678 )D247 - 678
12X-RAY DIFFRACTION12chain 'D' and (resid 679 through 1026 )D679 - 1026
13X-RAY DIFFRACTION13chain 'E' and (resid 247 through 660 )E247 - 660
14X-RAY DIFFRACTION14chain 'E' and (resid 661 through 1026 )E661 - 1026
15X-RAY DIFFRACTION15chain 'F' and (resid 246 through 678 )F246 - 678
16X-RAY DIFFRACTION16chain 'F' and (resid 679 through 1026 )F679 - 1026

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