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- PDB-8vdk: Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein ... -

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Basic information

Entry
Database: PDB / ID: 8vdk
TitleCrystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus
ComponentsSerine-aspartate repeat-containing protein D
KeywordsCELL ADHESION / microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) / LPXTG-motif / Center for Structural Biology of Infectious Diseases / CSBID / Structural Genomics
Function / homology
Function and homology information


SD-repeat containing protein, B domain / SdrD B-like domain / : / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...SD-repeat containing protein, B domain / SdrD B-like domain / : / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Serine-aspartate repeat-containing protein D
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus JH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Tan, A. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus
Authors: Kim, Y. / Tan, A. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionDec 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,68617
Polymers48,7131
Non-polymers97316
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.054, 72.825, 148.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine-aspartate repeat-containing protein D


Mass: 48713.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus JH1 (bacteria)
Strain: JH1 / Gene: sdrD, SAV0562 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q99W47
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M magnesium chloride, 0.08 TrisHCl pH8.5, 24 %(w/v) PEG4000, 20 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.33 Å / Num. obs: 44004 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3111 / CC1/2: 0.9 / Rpim(I) all: 0.228 / Rrim(I) all: 0.824 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.33 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 2124 4.84 %
Rwork0.1785 41803 -
obs0.18 43927 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 55 324 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353481
X-RAY DIFFRACTIONf_angle_d0.65644722
X-RAY DIFFRACTIONf_chiral_restr0.0518540
X-RAY DIFFRACTIONf_plane_restr0.0044617
X-RAY DIFFRACTIONf_dihedral_angle_d13.05461272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.27541460.24752639X-RAY DIFFRACTION97.79
1.84-1.890.26731350.22012759X-RAY DIFFRACTION100
1.89-1.940.2371390.1892771X-RAY DIFFRACTION99.97
1.94-20.23711270.17752738X-RAY DIFFRACTION100
2-2.060.19161450.17812787X-RAY DIFFRACTION100
2.06-2.140.2381490.17832728X-RAY DIFFRACTION99.97
2.14-2.220.23411350.1772772X-RAY DIFFRACTION100
2.22-2.320.1981440.17422742X-RAY DIFFRACTION99.97
2.32-2.450.19991240.18842806X-RAY DIFFRACTION100
2.45-2.60.24181520.19392782X-RAY DIFFRACTION100
2.6-2.80.2211500.212783X-RAY DIFFRACTION100
2.8-3.080.23481480.20172801X-RAY DIFFRACTION100
3.08-3.530.2441460.18032833X-RAY DIFFRACTION100
3.53-4.440.17411250.15482866X-RAY DIFFRACTION99.97
4.44-29.330.17391590.15832996X-RAY DIFFRACTION99.87
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)
10.843859387611-0.105371338129-0.7182476291861.351696618620.5849926912491.55264377404-0.00577618661793-0.06195460625470.01175579326060.147578141985-0.0537320706316-0.0140300339391-0.05157423754960.05457897812550.05843641721020.214097388158-0.0309999890805-0.0421234476490.2238613626340.02394366201570.21329294579711.4015141653-3.16493575737-15.9348726511
23.452694177812.009614381-1.432792787614.20538409766-0.8215827238122.918629645270.313839464687-0.5470512065120.02818771977830.70362375132-0.2747749850090.0217058953572-0.3239440790120.1246571029070.02010178529770.363155235039-0.0147486190923-0.008551998830820.2833768025350.001213507743060.205486130611-3.19015788829-4.1855553917511.5136233895
31.52810549823-0.503821532287-2.03750549730.5065763363680.9477979481344.049991269710.123436168080.02825413866990.1584360538850.05523949053460.00720133945691-0.0650112756737-0.139189908052-0.2906859705350.07787087404780.1967326804510.0184992598233-0.03987114382450.1977184297130.03468922318350.221741880664-4.36046996554-11.1157778435-12.9895958777
43.02023887526-0.271099432627-0.2268647315741.82618491880.03216274255161.480221430980.04439194170120.08565016979590.137333191155-0.0875622646906-0.0795725155431-0.03667312462320.0274285854046-0.019467180890.02413434701320.1923767076190.01276059216-0.01432548787330.176936697523-0.02441286719140.1855268765745.42886869952-26.0819347297-44.2789516982
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 170 )1 - 1701 - 170
22chain 'A' and (resid 171 through 281 )171 - 281171 - 281
33chain 'A' and (resid 282 through 340 )282 - 340282 - 333
44chain 'A' and (resid 341 through 439 )341 - 439334 - 432

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