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- PDB-3gvm: Structure of the homodimeric WXG-100 family protein from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 3gvm
TitleStructure of the homodimeric WXG-100 family protein from Streptococcus agalactiae
ComponentsPutative uncharacterized protein SAG1039
KeywordsVIRAL PROTEIN / WXG motif / Four-helical bundle
Function / homologyESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / ESAT-6-like protein SAG1039
Function and homology information
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsPoulsen, C. / Gries, F. / Wilmanns, M. / Song, Y.H.
CitationJournal: Plos One / Year: 2014
Title: WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern.
Authors: Poulsen, C. / Panjikar, S. / Holton, S.J. / Wilmanns, M. / Song, Y.H.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein SAG1039
B: Putative uncharacterized protein SAG1039
C: Putative uncharacterized protein SAG1039
D: Putative uncharacterized protein SAG1039


Theoretical massNumber of molelcules
Total (without water)43,3554
Polymers43,3554
Non-polymers00
Water8,323462
1
A: Putative uncharacterized protein SAG1039
B: Putative uncharacterized protein SAG1039


Theoretical massNumber of molelcules
Total (without water)21,6782
Polymers21,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-36 kcal/mol
Surface area10830 Å2
MethodPISA
2
C: Putative uncharacterized protein SAG1039
D: Putative uncharacterized protein SAG1039


Theoretical massNumber of molelcules
Total (without water)21,6782
Polymers21,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-37 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.100, 132.530, 43.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative uncharacterized protein SAG1039 / SAG1039


Mass: 10838.833 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: 2603V/R / Gene: SAG1039 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q8DZR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 1.9M (NH4)SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONESRF ID2920.97921
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 2, 2008
ADSC QUANTUM 315r2CCDJul 29, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double channel-cut Si (111) monochromatorSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979211
ReflectionNumber: 138669 / Rmerge(I) obs: 0.04 / D res high: 2.5 Å / Num. obs: 50045 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
11.195050988.510.024
7.9111.19100796.110.022
6.467.91132697.610.026
5.66.46157498.110.032
55.6176796.610.031
4.575193097.110.027
4.234.57210996.910.029
3.964.23226197.810.03
3.733.9625049810.032
3.543.73257998.310.033
3.373.54270198.810.035
3.233.37290898.910.039
3.13.23295498.910.043
2.993.1311498.710.051
2.892.99320699.110.06
2.82.89339899.210.074
2.712.8341299.210.083
2.642.71355598.810.102
2.572.64358198.710.112
2.52.57365094.710.131
ReflectionResolution: 2.15→50 Å / Num. all: 43035 / Num. obs: 43011 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 31.776 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 19300 / Num. unique all: 3130 / Num. unique obs: 3128 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
Auto-Rickshawphasing
SADABSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→46.957 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.871 / SU ML: -0 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2150 5 %
Rwork0.183 --
obs0.185 42997 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.188 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 94.94 Å2 / Biso mean: 30.376 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.719 Å2-0 Å20 Å2
2---4.456 Å2-0 Å2
3---6.175 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 462 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083042
X-RAY DIFFRACTIONf_angle_d0.8864132
X-RAY DIFFRACTIONf_chiral_restr0.057489
X-RAY DIFFRACTIONf_plane_restr0.004553
X-RAY DIFFRACTIONf_dihedral_angle_d18.9881130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.2591400.2126672807100
2.2-2.2550.2531400.226612801100
2.255-2.3160.2521420.19126902832100
2.316-2.3840.2231410.18726882829100
2.384-2.4610.2061430.17926982841100
2.461-2.5490.2321410.18526902831100
2.549-2.6510.2241410.19326842825100
2.651-2.7720.2561430.20527052848100
2.772-2.9180.2651440.21827322876100
2.918-3.1010.191420.20327092851100
3.101-3.340.2191430.18127132856100
3.34-3.6760.21440.16527352879100
3.676-4.2080.191440.15427452889100
4.208-5.30.1831470.15528012948100
5.3-46.9680.2031550.1942929308499

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