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- PDB-4igb: Crystal structure of the N-terminal domain of the Streptococcus g... -

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Basic information

Entry
Database: PDB / ID: 4igb
TitleCrystal structure of the N-terminal domain of the Streptococcus gordonii adhesin Sgo0707
Components(LPXTG cell wall surface ...) x 4
KeywordsCELL ADHESION / Beta-sandwich folds / Adhesin / Collagen-binding / oral keratinocytes / Cell wall anchored protein
Function / homology
Function and homology information


SHIRT domain / Sgo0707, N-terminal domain / SHIRT domain / Sgo0707 N-terminal domain / Sgo0707-like, N2 domain / Sgo0707 N2 domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...SHIRT domain / Sgo0707, N-terminal domain / SHIRT domain / Sgo0707 N-terminal domain / Sgo0707-like, N2 domain / Sgo0707 N2 domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / LPXTG cell wall surface protein
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsNylander, A. / Svensater, G. / Senadheera, D.B. / Cvitkovitch, D.G. / Davies, J.R. / Persson, K.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Analysis of the N-terminal Domain of the Streptococcus gordonii Adhesin Sgo0707
Authors: Nylander, A. / Svensater, G. / Senadheera, D.B. / Cvitkovitch, D.G. / Davies, J.R. / Persson, K.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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 / struct_ref_seq_dif / struct_site
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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPXTG cell wall surface protein
B: LPXTG cell wall surface protein
C: LPXTG cell wall surface protein
D: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,95122
Polymers192,6054
Non-polymers1,34718
Water23,0951282
1
A: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4216
Polymers48,0541
Non-polymers3665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9045
Polymers48,5971
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0766
Polymers48,7101
Non-polymers3665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LPXTG cell wall surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5515
Polymers47,2431
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.131, 158.115, 164.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

21A-981-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 36:324 or resseq 331: 376 or...
211chain B and (resseq 36:324 or resseq 331: 376 or...
311chain C and (resseq 36:324 or resseq 331: 376 or...
411chain D and (resseq 36:324 or resseq 331: 376 or...

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Components

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LPXTG cell wall surface ... , 4 types, 4 molecules ABCD

#1: Protein LPXTG cell wall surface protein


Mass: 48054.316 Da / Num. of mol.: 1 / Fragment: Sgo0707-N, UNP residues 36-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: Challis / ATCC 35105 / CH1 / DL1 / V288 / Gene: SGO_0707 / Plasmid: PetM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8AW49
#2: Protein LPXTG cell wall surface protein


Mass: 48596.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: Challis / ATCC 35105 / CH1 / DL1 / V288 / Gene: SGO_0707 / Plasmid: PetM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8AW49
#3: Protein LPXTG cell wall surface protein


Mass: 48710.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: Challis / ATCC 35105 / CH1 / DL1 / V288 / Gene: SGO_0707 / Plasmid: PetM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8AW49
#4: Protein LPXTG cell wall surface protein


Mass: 47243.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: Challis / ATCC 35105 / CH1 / DL1 / V288 / Gene: SGO_0707 / Plasmid: PetM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8AW49

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Non-polymers , 5 types, 1300 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1282 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5652.03
2
Crystal growTemperature: 291.15 K
Details: 20%(w/v) PEG4000, 0.1M sodium acetate, 0.2M ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
PH range: 5.0; 5.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.9793
SYNCHROTRONESRF ID23-120.9793
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 30, 2010
MARMOSAIC 225 mm CCD2CCDDec 1, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→48.45 Å / Num. obs: 114889 / % possible obs: 98.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.09→2.2 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
DNAdata collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.09→41.07 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 5640 5.01 %
Rwork0.179 --
obs0.181 112615 96.5 %
all-114889 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.48 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9272 Å2-0 Å2-0 Å2
2---2.1994 Å2-0 Å2
3----0.7278 Å2
Refinement stepCycle: LAST / Resolution: 2.09→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13424 0 76 1282 14782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713718
X-RAY DIFFRACTIONf_angle_d1.10318608
X-RAY DIFFRACTIONf_dihedral_angle_d14.0755046
X-RAY DIFFRACTIONf_chiral_restr0.0712117
X-RAY DIFFRACTIONf_plane_restr0.0042422
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3129X-RAY DIFFRACTIONPOSITIONAL
12B3129X-RAY DIFFRACTIONPOSITIONAL0.711
13C3129X-RAY DIFFRACTIONPOSITIONAL1.081
14D3129X-RAY DIFFRACTIONPOSITIONAL1.182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.09-2.11340.32011240.2626228562
2.1134-2.13830.30711890.2345311986
2.1383-2.16440.30551740.228324789
2.1644-2.19180.29671740.2265335591
2.1918-2.22060.28591750.2212343894
2.2206-2.2510.30851650.2207355896
2.251-2.28320.27182110.1984353497
2.2832-2.31730.23231810.1905353997
2.3173-2.35350.26571910.1912355297
2.3535-2.39210.24112020.1974358798
2.3921-2.43330.28572060.1874360598
2.4333-2.47750.25541840.1871359498
2.4775-2.52520.25271950.1896360898
2.5252-2.57670.23881690.1801367499
2.5767-2.63270.23861730.1754365499
2.6327-2.6940.24041850.1881364699
2.694-2.76130.26371820.1803366099
2.7613-2.8360.22551970.1827365399
2.836-2.91940.23871910.1831368899
2.9194-3.01360.24462110.18513627100
3.0136-3.12130.22161950.18713717100
3.1213-3.24620.22351920.19023676100
3.2462-3.39390.22652120.18583671100
3.3939-3.57270.23462010.18593694100
3.5727-3.79640.22331880.17163752100
3.7964-4.08930.1841760.15533715100
4.0893-4.50030.17362010.13353733100
4.5003-5.15050.15511870.12983757100
5.1505-6.48490.18972040.17193789100
6.4849-41.07420.21322050.2026384898
Refinement TLS params.Method: refined / Origin x: 38.8013 Å / Origin y: -1.643 Å / Origin z: 41.6425 Å
111213212223313233
T0.092 Å20.0095 Å2-0.003 Å2-0.0875 Å2-0.0104 Å2--0.0878 Å2
L0.1563 °20.0353 °20.0142 °2-0.1336 °2-0.0404 °2--0.0414 °2
S-0.0022 Å °0.0225 Å °-0.0431 Å °0.0257 Å °-0.0143 Å °-0.026 Å °-0.0024 Å °0.004 Å °0.0074 Å °
Refinement TLS groupSelection details: all

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