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- PDB-7qld: Crystal structure of S-layer protein SlpA from Lactobacillus acid... -

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Basic information

Entry
Database: PDB / ID: 7qld
TitleCrystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I, Co-crystallization with HgCl2, Mutation Ser146Cys, (aa 32-198)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / SlpA / Surface Layer Protein / S-layer / self-assembly / Lactobacillus acidophilus
Function / homologyLactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region / : / S-layer protein
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.153 Å
AuthorsSagmeister, T. / Vejzovic, D. / Eder, M. / Dordic, A. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29432 Austria
CitationJournal: To Be Published
Title: The self-assembly of the S-layer protein from Lactobacilli acidophilus
Authors: Sagmeister, T. / Eder, M. / Grininger, C. / Vejzovic, D. / Buhlheller, C. / Dordic, A. / Damisch, E. / Millan, C. / Medina, A. / Uson, I. / Baek, M. / Read, R. / Baker, D. / Pavkov-Keller, T.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: S-layer protein
A: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0628
Polymers34,5192
Non-polymers5436
Water1,27971
1
B: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5314
Polymers17,2601
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5314
Polymers17,2601
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.360, 85.360, 191.965
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111B30 - 193
221A30 - 193

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein S-layer protein / / Surface layer protein / SA-protein


Mass: 17259.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpA, LBA0169 / Production host: Escherichia coli (E. coli) / References: UniProt: P35829
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with ...Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop and co-crystallization with 0.1 ul 2mM HgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→48.38 Å / Num. obs: 23300 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.87-48.387.40.0294320.9990.0140.033
2.15-2.2210.60.85919480.8910.3950.947

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.153→48.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.377 / SU ML: 0.156 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2663 1153 4.963 %
Rwork0.2189 22078 -
all0.221 --
obs-23231 99.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.531 Å20.765 Å20 Å2
2--1.531 Å2-0 Å2
3----4.966 Å2
Refinement stepCycle: LAST / Resolution: 2.153→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 6 71 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132256
X-RAY DIFFRACTIONr_bond_other_d0.0060.0152105
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6433079
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5784828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5327.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215329
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg18.248152
X-RAY DIFFRACTIONr_chiral_restr0.0660.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
X-RAY DIFFRACTIONr_nbd_refined0.2110.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.21737
X-RAY DIFFRACTIONr_nbtor_refined0.150.21140
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.213
X-RAY DIFFRACTIONr_nbd_other0.1420.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.30.28
X-RAY DIFFRACTIONr_mcbond_it5.6026.8121258
X-RAY DIFFRACTIONr_mcbond_other5.5856.8091257
X-RAY DIFFRACTIONr_mcangle_it7.46210.1661562
X-RAY DIFFRACTIONr_mcangle_other7.46110.1711563
X-RAY DIFFRACTIONr_scbond_it6.6587.332998
X-RAY DIFFRACTIONr_scbond_other6.6357.331995
X-RAY DIFFRACTIONr_scangle_it8.86610.7571517
X-RAY DIFFRACTIONr_scangle_other8.86310.7611518
X-RAY DIFFRACTIONr_lrange_it10.91481.2442206
X-RAY DIFFRACTIONr_lrange_other10.92181.1972201
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.053942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.119750.05008
12AX-RAY DIFFRACTIONLocal ncs0.119750.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.2080.364720.3271591X-RAY DIFFRACTION99.2836
2.208-2.2690.28790.3081545X-RAY DIFFRACTION100
2.269-2.3350.423880.321503X-RAY DIFFRACTION100
2.335-2.4060.27800.2821466X-RAY DIFFRACTION100
2.406-2.4850.329830.2751406X-RAY DIFFRACTION100
2.485-2.5720.307770.2571393X-RAY DIFFRACTION100
2.572-2.6690.357630.2871353X-RAY DIFFRACTION99.9294
2.669-2.7770.385770.2711267X-RAY DIFFRACTION100
2.777-2.90.3680.2641231X-RAY DIFFRACTION100
2.9-3.0410.298660.2521200X-RAY DIFFRACTION100
3.041-3.2050.273560.2371142X-RAY DIFFRACTION100
3.205-3.3990.305450.2551087X-RAY DIFFRACTION100
3.399-3.6320.367560.2621019X-RAY DIFFRACTION100
3.632-3.9210.278540.23948X-RAY DIFFRACTION99.9003
3.921-4.2930.203380.181904X-RAY DIFFRACTION100
4.293-4.7950.171290.131826X-RAY DIFFRACTION99.8832
4.795-5.5270.197390.159724X-RAY DIFFRACTION99.7386
5.527-6.7480.272370.186635X-RAY DIFFRACTION100
6.748-9.4510.19250.179510X-RAY DIFFRACTION100
9.451-48.380.223210.241328X-RAY DIFFRACTION99.7143

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