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- PDB-5cqv: Crystal structure of uncharacterized protein Q8DWV2 from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 5cqv
TitleCrystal structure of uncharacterized protein Q8DWV2 from Streptococcus agalactiae
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / DUF1706 / DfsB
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / ClbS/DfsB family four-helix bundle protein
Function and homology information
Biological speciesStreptococcus agalactiae serotype V
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTaylor, J.D. / Hare, S. / Matthews, S.J.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.
Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4734
Polymers43,2372
Non-polymers2362
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-74 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 65.930, 55.750
Angle α, β, γ (deg.)90.00, 114.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 21618.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria)
Gene: SAG2111 / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DWV2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M Diethylene glycol, 0.12 M Triethylene glycol, 0.12 M Tetraethylene glycol, 0.12 M Pentaethylene glycol, 0.1 M Tris, 0.1 M Bicine, pH 8.5, 5% MPD, 12% PEG 550 MME, 6% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.9→20.16 Å / Num. obs: 26530 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
xia2data reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COM

5com


Resolution: 1.9→20.16 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2187 1343 5.07 %
Rwork0.1779 --
obs0.1801 26510 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 16 166 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082952
X-RAY DIFFRACTIONf_angle_d1.0994009
X-RAY DIFFRACTIONf_dihedral_angle_d15.0251111
X-RAY DIFFRACTIONf_chiral_restr0.042442
X-RAY DIFFRACTIONf_plane_restr0.005501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.9680.26921370.24532484X-RAY DIFFRACTION98
1.968-2.04670.2581460.21962516X-RAY DIFFRACTION99
2.0467-2.13970.23971250.2022504X-RAY DIFFRACTION98
2.1397-2.25240.24311220.18732459X-RAY DIFFRACTION96
2.2524-2.39330.22731330.17472505X-RAY DIFFRACTION99
2.3933-2.57780.25341200.18592555X-RAY DIFFRACTION99
2.5778-2.83650.23111430.18242537X-RAY DIFFRACTION99
2.8365-3.24550.23391370.18112499X-RAY DIFFRACTION97
3.2455-4.08340.18171380.15952534X-RAY DIFFRACTION99
4.0834-20.16130.20321420.16542574X-RAY DIFFRACTION98
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)
11.3399-0.6489-0.90390.90940.86582.3685-0.06910.1615-0.1157-0.0938-0.05430.09780.1166-0.20440.08170.16010.00380.00670.1250.04720.160119.57888.84652.5503
24.46732.90891.10493.18490.18321.169-0.04490.4932-0.2502-0.5425-0.55470.11110.3131-1.59570.70671.3966-0.09750.16631.2589-0.15860.81885.4846-5.3655-0.5942
30.6242-0.25390.02451.91011.27923.5576-0.0875-0.0548-0.05490.286-0.34140.34950.4069-1.0138-0.15250.1799-0.01110.03710.2113-0.00610.195819.13931.23331.1269
40.2816-0.6693-0.18141.50520.37032.310.09550.2097-0.13310.1683-0.06280.14550.1073-0.32150.06240.1570.018-0.03340.343-0.01790.160319.793111.9637-12.9695
52.2881-0.9131-0.67220.82190.64031.93360.0928-0.04270.2005-0.077-0.06930.119-0.2992-0.6213-0.03350.26230.0623-0.00430.3628-0.01340.231119.814220.0542-17.8193
64.6541-3.7361-2.18374.60431.75761.0735-0.2782-0.0373-0.8825-0.64221.2301-0.25470.49730.4349-0.9120.7340.0174-0.0091.4941-0.13881.06995.71088.5916-27.9747
74.3693-1.8952-1.28776.85824.63195.96220.02441.1912-1.3364-0.8154-0.98370.30540.3031-1.04220.80560.5784-0.01780.02360.9247-0.10180.63820.532914.3228-30.42
82.82640.1445-0.65520.84120.8611.22930.1477-0.08560.787-0.5605-0.39420.3556-0.7567-1.4534-1.01650.12740.405-0.03081.0304-0.01410.33688.119123.0871-16.4735
91.6483-1.08581.50951.7226-0.98842.01190.30840.0009-0.27490.1888-0.1470.78380.6484-1.1225-0.17020.4593-0.0648-0.01690.9231-0.19170.57265.70896.0348-17.135
101.2998-1.146-1.58513.47422.55552.79950.09750.21250.0109-0.1254-0.25920.3319-0.1997-0.5170.05380.18540.0253-0.01160.14610.04890.145517.673115.53470.7385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 142 )
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 184 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 142 )
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 184 )

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