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- PDB-4de8: LytR-Cps2a-Psr family protein with bound octaprenyl monophosphate... -

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Basic information

Entry
Database: PDB / ID: 4de8
TitleLytR-Cps2a-Psr family protein with bound octaprenyl monophosphate lipid
ComponentsCps2A
KeywordsMEMBRANE PROTEIN / Possible wall techoic acid synthesis
Function / homology
Function and homology information


DNA replication / membrane
Similarity search - Function
LCP protein / DNA polymerase processivity factor / Cell envelope-related transcriptional attenuator domain / DNA polymerase processivity factor / LytR_cpsA_psr family / Aminopeptidase / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0K3 / DI(HYDROXYETHYL)ETHER / Cps2A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEberhardt, A. / Hoyland, C.N. / Vollmer, D.V. / Bisle, S. / Cleverley, R.M. / Johnsborg, O. / Havarstein, L.S. / Lewis, R.J. / Vollmer, W.
CitationJournal: Microb Drug Resist / Year: 2012
Title: Attachment of Capsular Polysaccharide to the Cell Wall in Streptococcus pneumoniae.
Authors: Eberhardt, A. / Hoyland, C.N. / Vollmer, D. / Bisle, S. / Cleverley, R.M. / Johnsborg, O. / Havarstein, L.S. / Lewis, R.J. / Vollmer, W.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Cps2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5293
Polymers43,7801
Non-polymers7492
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.187, 73.187, 163.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cps2A / Integral membrane regulatory protein Cps2A


Mass: 43779.938 Da / Num. of mol.: 1 / Fragment: UNP residues 98-481 / Mutation: R267A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / NCTC 7466 / Gene: cps2A, SPD_0315 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9ZII9
#2: Chemical ChemComp-0K3 / (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate


Mass: 642.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H67O4P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M diammonium citrate 15% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→19.72 Å / Num. all: 33316 / Num. obs: 33316 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 16.1 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 8.8 / Num. unique all: 4749 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.72 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 20.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1683 5.06 %RANDOM
Rwork0.1892 ---
all0.1912 33253 --
obs0.1912 33253 99.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.89 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2499 Å20 Å2-0 Å2
2--3.2499 Å2-0 Å2
3----6.4999 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 52 134 3079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043027
X-RAY DIFFRACTIONf_angle_d0.7824107
X-RAY DIFFRACTIONf_dihedral_angle_d12.5361143
X-RAY DIFFRACTIONf_chiral_restr0.046480
X-RAY DIFFRACTIONf_plane_restr0.003532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00730.25161300.20662542X-RAY DIFFRACTION100
2.0073-2.07210.24121460.20912615X-RAY DIFFRACTION100
2.0721-2.1460.2131340.19292568X-RAY DIFFRACTION100
2.146-2.23190.26351380.1862585X-RAY DIFFRACTION100
2.2319-2.33330.22651470.19262595X-RAY DIFFRACTION100
2.3333-2.45610.25821320.192611X-RAY DIFFRACTION100
2.4561-2.60960.22651450.20412593X-RAY DIFFRACTION100
2.6096-2.81060.25431680.21132598X-RAY DIFFRACTION100
2.8106-3.09250.28091450.21112628X-RAY DIFFRACTION100
3.0925-3.53770.22941370.2022662X-RAY DIFFRACTION100
3.5377-4.44870.20481270.162710X-RAY DIFFRACTION100
4.4487-19.72280.20111340.17792863X-RAY DIFFRACTION100
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)
12.88970.5681-0.97311.2640.14961.9764-0.32961.1772-0.6409-0.32620.4004-0.24930.16410.19860.06990.1866-0.04120.12180.4285-0.11490.18443.686-1.093620.7256
20.6413-0.1908-0.20460.12730.06650.0881-0.16541.0228-0.0306-0.48050.08960.40980.07530.0345-0.04430.1808-0.19390.15560.50.1764-0.1197-10.57393.923118.8053
33.97941.5059-0.42883.2072-0.662.284-0.02390.08420.24580.1008-0.1151-0.0536-0.08890.06310.14240.1567-0.0179-0.03060.11670.01430.1526-30.59075.321424.6168
41.7037-1.02410.52761.087-0.81722.5095-0.03680.21270.0249-0.0557-0.1204-0.114-0.10440.28080.11920.1517-0.0373-0.02370.11330.02250.1391-22.90291.506426.0203
51.7477-0.331-0.52042.0011-1.32963.0865-0.0431-0.16140.16610.2591-0.0801-0.0255-0.36620.06920.09830.2391-0.0329-0.07130.12730.01710.1666-34.806114.721629.8512
63.05340.01870.92891.3483-0.47761.76980.0792-0.4262-0.5573-0.03580.06540.25380.2422-0.3699-0.13680.2268-0.03960.01770.18210.03030.2519-30.6511-5.910632.7467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 111:195)
2X-RAY DIFFRACTION2chain 'A' and (resseq 196:224)
3X-RAY DIFFRACTION3chain 'A' and (resseq 225:264)
4X-RAY DIFFRACTION4chain 'A' and (resseq 265:324)
5X-RAY DIFFRACTION5chain 'A' and (resseq 325:428)
6X-RAY DIFFRACTION6chain 'A' and (resseq 429:484)

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