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- PDB-9f8e: SLPL/SLPH (H/L) complex from C. difficile SlpA (Ox247_delta_orf2 ... -

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Basic information

Entry
Database: PDB / ID: 9f8e
TitleSLPL/SLPH (H/L) complex from C. difficile SlpA (Ox247_delta_orf2 strain, SLCT11)
Components(S-layer protein) x 2
KeywordsSTRUCTURAL PROTEIN / S-layer / SlpA / C. difficile / SLLP
Function / homology: / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / S-layer protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBarwinska-Sendra, A. / Salgado, P.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V032151/1 United Kingdom
CitationJournal: To Be Published
Title: SLPL/SLPH (H/L) complex from C. difficile SlpA (Ox247 strain)
Authors: Barwinska-Sendra, A. / Salgado, P.S.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-layer protein
B: S-layer protein
C: S-layer protein
D: S-layer protein


Theoretical massNumber of molelcules
Total (without water)124,7444
Polymers124,7444
Non-polymers00
Water30617
1
A: S-layer protein
B: S-layer protein


Theoretical massNumber of molelcules
Total (without water)62,3722
Polymers62,3722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-layer protein
D: S-layer protein


Theoretical massNumber of molelcules
Total (without water)62,3722
Polymers62,3722
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.612, 73.374, 90.799
Angle α, β, γ (deg.)91.640, 95.740, 96.110
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 36 or resid 43 through 178))
d_2ens_1(chain "C" and (resid 1 through 123 or resid 128 through 178))
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALALEULEUAA1 - 361 - 36
d_12ens_1LEULEUPHEPHEAA43 - 17843 - 178
d_21ens_1ALAALAVALVALCC1 - 1231 - 123
d_22ens_1LYSLYSPHEPHECC128 - 178128 - 178
d_11ens_2THRTHRMETMETBB5 - 4075 - 407
d_21ens_2THRTHRMETMETDD5 - 4075 - 407

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.636491226846, -0.769253841946, 0.0559235621161), (-0.766770475201, -0.638933667596, -0.0618611895542), (0.0833184043798, -0.0035064318652, -0.9965168079)14.8420674149, 32.6439376498, -7.4471752589
2given(0.531553286277, -0.829708777766, 0.170394976296), (-0.829252212572, -0.55075460109, -0.094921743152), (0.172603220692, -0.0908444465929, -0.980793257894)18.5016608392, 32.4844891993, -7.83999570695

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Components

#1: Protein S-layer protein


Mass: 19528.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SLPL - SlpA LMW protein from C. difficile strain Ox247 delta-orf2
Source: (natural) Clostridioides difficile (bacteria) / Variant: delta orf2 / Strain: Ox247 / References: UniProt: Q2N3V9
#2: Protein S-layer protein


Mass: 42843.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Variant: delta orf2 / Strain: Ox247 / References: UniProt: Q2N3V9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4mM Oxometalates, 0.05M Tris (base), 0.o5M BICINE, 20% v/v Glycerol; 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.70846 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70846 Å / Relative weight: 1
ReflectionResolution: 3.1→39.08 Å / Num. obs: 21675 / % possible obs: 96.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.407 / CC star: 0.76 / Rrim(I) all: 0.43 / Net I/σ(I): 7.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2166 / CC1/2: 0.159 / CC star: 0.524 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→39.08 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.5127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1058 4.95 %
Rwork0.1785 20296 -
obs0.1813 21675 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.79 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8618 0 0 17 8635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328694
X-RAY DIFFRACTIONf_angle_d0.582311769
X-RAY DIFFRACTIONf_chiral_restr0.04171434
X-RAY DIFFRACTIONf_plane_restr0.00571519
X-RAY DIFFRACTIONf_dihedral_angle_d5.05191212
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.3758755042
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.721985274658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.26581420.22592432X-RAY DIFFRACTION93.4
3.24-3.410.30791470.21282494X-RAY DIFFRACTION95
3.41-3.630.24421340.20542485X-RAY DIFFRACTION95.03
3.63-3.910.22681270.18422491X-RAY DIFFRACTION95.69
3.91-4.30.22281240.17012598X-RAY DIFFRACTION97.7
4.3-4.920.22181370.14972574X-RAY DIFFRACTION99.01
4.92-6.190.22061210.17032597X-RAY DIFFRACTION99.27
6.19-39.080.19111260.15212625X-RAY DIFFRACTION99.46
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3402716984250.4247135405070.3691883956610.855157026441-0.1163698198381.09297067856-0.09964007280560.432037616542-0.451817860248-0.1541530958970.08487373010320.04394852815160.144850258659-0.309500918564-0.08540424728010.3167138723940.0629859692551-0.006877304169790.3675106448130.1003999759440.354798795569-4.893336234534.32972469944-48.5807833695
20.913520848520.0193055871518-0.4886721598680.372655822301-0.08022499159881.13619841117-0.425342245319-0.08717586648440.2913474211610.1671952316280.1625600351550.611750384668-0.00456174761163-0.3793136227810.0627141681426-0.7651582728340.306538337541-0.8354835726150.6268154933540.467790876454-0.048359377766-12.67777139049.16252068861-56.9933389298
30.504867105808-0.35088915582-0.2782949263870.5453046750260.2244489494780.7303448515640.246632899071-0.8019759973090.01358797827660.0870903153267-0.106060273735-0.444752376854-0.396662277641-0.199271708768-0.09572359439450.5510579035680.1132813476470.03998988592750.32317793760.07134390163320.40999137589-3.3898845972818.7676931818-33.0267961516
40.439583157192-0.3414034208761.135613246080.327551208277-0.9323859425032.668713008960.064615736086-0.4468049251970.0410248462156-0.2378500832720.1371879209460.248518717631-0.196093189702-0.550746071665-0.02408845556690.9279809866940.151948481936-0.2070352552650.3610958971910.1246750977570.32150244279-2.8271993309420.6032815265-49.0863448208
50.257574242331-0.254657987582-0.09113408665210.797976458592-0.2497747587490.809913419761-0.3380922361550.3438044793730.2792498757790.2985692797730.3644207789350.4341743897-0.809832717215-0.0500618670288-0.09266499627670.610941366957-0.133827463609-0.0911787454710.5167584311160.02809720663370.126850880759-2.6976047920612.0408469766-44.3658011454
60.7022167838940.984913344359-0.1863661313171.861463103080.1303763286260.301440972714-0.211924967477-0.613480024060.0471384838561-0.07174531900610.1726337501390.01041708101180.8269962916380.502171843215-0.1124437987010.4119673510350.134269002028-0.009220864547830.3843730414680.06533079161190.3300358047168.31654183989-7.08369150552-34.5448153635
72.708822787440.1438425851420.2429015690322.05090915399-0.2027479700021.9973603353-0.201211862518-0.5034670434180.157392448654-0.2115454286860.2672325678140.05912707319370.943370614827-0.0271516147292-0.2037516673260.403491886744-0.008003282027860.01430642274810.2459950917440.008702914667180.2080968425871.15061973991-5.36144493543-25.7340217587
82.585280065660.0706307237992-0.6196775315280.9114301434990.9338752510051.326677320820.6391957397060.730607872292-0.094989592818-0.316373365064-0.160251355340.7228654965180.162188982883-0.0137796894761-0.05163103840131.14665589603-0.324909888666-0.1208443810670.796926110356-0.04807268506990.416672295326-7.21407554996-15.7755114166-38.078190706
90.408185820123-0.00763883598593-0.3238596604850.734991493791-0.7133704885370.7278663438370.568879623086-0.07180470362-0.154557688269-0.501308387742-0.0576240769062-0.8109984478740.972091505787-0.0721442739965-0.1030573105680.542893552641-0.0273023737162-0.1575765441980.229945676303-0.01323086552840.1816569210915.33167243774-2.96381710793-28.7841458665
100.2310543392860.2782893791430.3971705691870.177230858817-0.3659101267831.0114877526-0.003845294160110.106764612507-0.0225860621631-0.2032520315430.05823010530420.04794781889620.512533438519-0.140409208024-0.126444743040.4047769577840.00236437782850.006215971645060.2915083982240.004054079715290.2060889288382.02779879987-6.02985561878-27.6364842052
111.554636829360.944291923886-0.1453254442371.776854914810.1678870433531.553085099410.0230256005675-0.08756268228010.04897295419770.155434737677-0.0282206559047-0.1379123399310.06506787599260.02817404656950.02618394211870.09294158228350.0322235333422-0.008234621413070.148752741954-0.0121299655370.163731846596.618389620662.3896473616715.430757165
120.715843789020.614675340146-0.4364768152261.494735836050.02065940080682.331281965240.0274662456651-0.183342969462-0.2463436750310.06049285589020.0755502580669-0.02535133507710.292430805251-0.0894221922536-0.0806963330350.09531352211970.00637885918234-0.01718467671760.15030512087-0.01884463109190.225938178307-5.90661242852-12.880900081511.1175483526
131.94669161140.4816122781770.07805031773561.837121633250.7420274201321.392488312970.1888149083880.307400678556-0.187674610728-0.122942329116-0.0726167531389-0.3804956102440.07700956556330.218746295263-0.1827378131080.11505361390.02621244315240.02472452512120.1967391476710.02765399772830.2552245286842.33396990305-11.4550989439-1.17483369846
142.20900615553-0.130231332385-0.6381441203090.2177541038740.4968459194240.5436821103330.0530903742375-0.5194680592230.08242319806810.0424835882696-0.3325621227430.308380488036-0.146603827371-0.1690964094020.1719148264590.668641626247-0.147057942330.1007244844820.447066260354-0.05073742431620.2895416155283.401315172336.898311258941.3886465594
150.368712395520.0576898636083-0.912660750252-0.036560581529-0.1250550775682.499547107630.7990071741140.016283450862-0.1960699418070.6997483961280.2510592163380.4043322042860.261933357855-0.229387943051-0.1071635689530.3176214673790.0646628672320.2872401806310.559605415154-0.2023159443090.380791822509-2.0087767869824.209924680827.3294599124
161.7803300123-0.398579928280.4188303803251.36761885488-0.4831606546681.045640609450.0885772126765-0.05161955016870.3128629670410.425539351333-0.4469338248410.586997608840.00586583470207-0.9468137028960.1054752045070.351131809351-0.109524568910.1042982955060.4503282698780.03985888571990.548411582884-6.1322905553923.758176378827.776449237
170.610661656526-0.364208851287-0.4641623421980.2437998265320.2986219198810.377869590963-0.0241941184875-0.250378175265-0.09598234490030.386692417493-0.104602945595-0.3555232996390.306277329710.01807387053140.03451915807950.848834093678-0.5177474504241.095104307010.7752057132670.10563210115-0.975687433555-3.143712810324.953368685145.801401849
180.44263589978-0.1683313337370.9676784588690.0570370621211-0.3578759365722.345088193940.7428465042210.0852447548441-0.917784927770.272824861748-0.147041979341-0.2300267535460.5353993709960.59520430776-0.01177863638731.06206168543-0.3194138755410.2090549061480.2550124048680.1835044433860.1891353022375.8741776532220.8514736135.6364391082
191.39809187009-0.7323119385450.237300397952.467234597030.7647681677251.824725046870.2348373690360.2277585141850.06839186001830.382717013652-0.5742573339520.417691763168-0.755109416748-0.5573252556110.04073366931550.611200357343-0.003828318774990.1448655350410.242641393878-0.09004809722450.281641359591-1.4042709414836.288003318535.2602385341
201.55786693789-0.248578852653-0.1310616798641.93315793704-0.1860862461931.53232164342-0.1160205332040.2593577135210.214300771757-0.0813288645101-0.000413753822286-0.627370027117-0.1865050695480.4168504812960.1037627029530.39742407247-0.1230784941850.01975303066690.332361597587-0.001978170316770.3915046226921.275848056935.845693199621.5193039703
210.965755029562-0.123003150582-1.0505522850.04234273132520.1925235392981.12637882670.039297349724-0.76702483493-0.06248604566950.1902780599330.1919224678950.380507835551-0.185446486184-0.17353909120.04322408770791.33135939764-0.384426267099-0.07710303889490.596766625542-0.1995400582220.11403796429921.335175487450.474065728130.2459851821
220.08742995006050.218842158729-0.2578512726120.958491798020.1306494361070.2318277712070.4953872260250.36490777397-1.055160308080.6896821379310.578887198205-0.144520380869-0.1942711526641.00480917844-0.104677440006-0.312252693663-0.6689284221750.4802928368180.1808523870450.202868799979-0.011923635203918.935746224332.24830263521.8100700411
230.1468017970130.1500756376520.401641484731-0.0716982017945-0.03667291486990.363621479564-0.0609490149277-0.3534102826450.3409004917970.2478812204880.358985491844-0.9920060630160.006629239617450.1841265115640.003822824388770.404935918883-0.31230235840.1912594251920.2143739887940.235081897418-0.10500654547821.479614814932.163906004712.8298003426
240.713715310927-0.1816813843820.1027875707041.28512661248-0.4164710382590.9880830617680.149829845025-0.3169362633480.518118565470.0694625282882-0.1778455268240.00488888175047-0.0931027637549-0.00883299337830.04577901448380.285820935389-0.0750540730330.03373283020530.290681583456-0.1583673653180.39539307366718.679323537524.4626494976-16.67799658
251.162982168591.80593575342-0.07324210600782.32690586395-0.4828068518351.09981127976-0.03921592579060.2044372414-0.300007153144-0.367420777104-0.07448341278-0.2685989600630.285700717211-0.0338323194310.2007099303780.4230198777110.0256565632342-0.00890451656390.285826821956-0.04822471616290.22054146915623.094697060518.2680724842-24.8467197287
262.934732646280.334811531411-0.6303441779552.044592609540.3311507618242.28464766655-0.1402418058470.8011943330550.413104941589-0.312638012924-0.08314239894520.365073610167-0.353602805264-0.1562418557430.06036318850970.3860144146160.0902606668954-0.0687641204980.206071854671-0.00727499742060.32458979301524.23435538836.9016276761-24.9055312586
271.270374326270.941172358437-0.0565354559522.07302389596-0.1182880989322.7046486217-0.0455226907809-0.05220112082780.428324791704-0.497529975017-0.04800840398240.114411271492-0.1169262437470.0331735214410.02229656357880.2333331784610.0213626081333-0.0356739984190.20707727863-0.05904822948980.41278953271227.923348454342.805403289-20.4547257701
281.241030295350.6743532435970.3106030811181.56886229167-0.6145495914231.550757611510.129762633354-0.317790725813-0.2001556099430.379526214583-0.255867428293-0.05659061221640.06983378338050.0245477355910.06823040742910.241428954702-0.01984395950350.0003609257069710.153504135314-0.0364288765170.27271551221628.99611667137.0089916304-5.20421737006
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 34 )AA1 - 341 - 34
22chain 'A' and (resid 35 through 47 )AA35 - 4735 - 47
33chain 'A' and (resid 48 through 67 )AA48 - 6748 - 67
44chain 'A' and (resid 68 through 80 )AA68 - 8068 - 80
55chain 'A' and (resid 81 through 114 )AA81 - 11481 - 114
66chain 'A' and (resid 115 through 129 )AA115 - 129115 - 125
77chain 'A' and (resid 130 through 152 )AA130 - 152126 - 148
88chain 'A' and (resid 153 through 162 )AA153 - 162149 - 158
99chain 'A' and (resid 163 through 178 )AA163 - 178159 - 174
1010chain 'B' and (resid 5 through 50 )BB5 - 501 - 46
1111chain 'B' and (resid 51 through 251 )BB51 - 25147 - 247
1212chain 'B' and (resid 252 through 338 )BB252 - 338248 - 334
1313chain 'B' and (resid 339 through 407 )BB339 - 407335 - 403
1414chain 'C' and (resid 1 through 47 )CC1 - 471 - 41
1515chain 'C' and (resid 48 through 57 )CC48 - 5742 - 51
1616chain 'C' and (resid 58 through 72 )CC58 - 7252 - 66
1717chain 'C' and (resid 73 through 83 )CC73 - 8367 - 77
1818chain 'C' and (resid 84 through 94 )CC84 - 9478 - 88
1919chain 'C' and (resid 95 through 113 )CC95 - 11389 - 107
2020chain 'C' and (resid 114 through 152 )CC114 - 152108 - 146
2121chain 'C' and (resid 153 through 162 )CC153 - 162147 - 156
2222chain 'C' and (resid 163 through 178 )CC163 - 178157 - 172
2323chain 'D' and (resid 5 through 66 )DD5 - 661 - 62
2424chain 'D' and (resid 67 through 115 )DD67 - 11563 - 111
2525chain 'D' and (resid 116 through 202 )DD116 - 202112 - 198
2626chain 'D' and (resid 203 through 244 )DD203 - 244199 - 240
2727chain 'D' and (resid 245 through 338 )DD245 - 338241 - 334
2828chain 'D' and (resid 339 through 407 )DD339 - 407335 - 403

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