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- PDB-3tel: LytR-CPS2A-Psr family protein with bound octaprenyl pyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 3tel
TitleLytR-CPS2A-Psr family protein with bound octaprenyl pyrophosphate lipid and manganese ion
ComponentsCps2A, Integral membrane regulatory protein Wzg
KeywordsTRANSFERASE / cell wall techoic acid synthesis / REPLICATION
Function / homology
Function and homology information


DNA replication / membrane / metal ion binding
Similarity search - Function
LCP protein / DNA polymerase processivity factor / DNA polymerase processivity factor / : / Cell envelope-related transcriptional attenuator domain / 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
ACETATE ION / : / Chem-ZTP / Integral membrane regulatory protein Wzg
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Khai Bui, N. / Hoyland, C.N. / Ogasawara, N. ...Kawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Khai Bui, N. / Hoyland, C.N. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J.
CitationJournal: Embo J. / Year: 2011
Title: A widespread family of bacterial cell wall assembly proteins.
Authors: Kawai, Y. / Marles-Wright, J. / Cleverley, R.M. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Bui, N.K. / Hoyland, C.N. / Ogasawara, N. / Lewis, R.J. / Vollmer, W. / Daniel, R.A. / Errington, J.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: 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

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Assembly

Deposited unit
A: Cps2A, Integral membrane regulatory protein Wzg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11110
Polymers43,9111
Non-polymers1,2009
Water6,377354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.681, 73.681, 163.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cps2A, Integral membrane regulatory protein Wzg


Mass: 43911.133 Da / Num. of mol.: 1 / Mutation: R270A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Description: plasmid / Gene: wzg, SPC02_0004 / Plasmid details: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K376

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Non-polymers , 5 types, 363 molecules

#2: Chemical ChemComp-ZTP / (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 trihydrogen diphosphate


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS ...THE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS DETECTED BY MASS SPECTROSCOPY; THE MASS SPECTROSCOPY DATA DO NOT RULE OUT THE PRESENCE OF OTHER POLYPRENOL PYROPHOSPHATE LIGANDS IN THE SAME BINDING SITE. THE LIGAND HAS BEEN MODELLED WITH THE SEVEN CHIRAL DOUBLE BONDS IN THE CIS CONFIGURATION, AS OCCUR IN THE EQUIVALENT DOUBLE BONDS IN THE LIPID CHAIN OF THE NATURALLY OCCURING SUBSTRATE OF THE ENZYME. THE ELECTRON DENSITY CAN ALSO ACOMMODATE DITRANSPENTACISOCTAPRENYL PYROPHOSPHATE{IUPAC NAME[(2Z,6Z,10Z,14Z,18Z,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL] PHOSPHONOHYDROGEN PHOSPHATE}, AN INTERMEDIATE IN THE SYNTHESIS OF UNDECAPRENYL PYROPHOSPHATE.

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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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6 9% PEG 4K, Cryprotectant solution containing 10 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2010
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→19.83 Å / Num. all: 42582 / Num. obs: 42582 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.9 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.182 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21978 2149 5.1 %RANDOM
Rwork0.18116 ---
obs0.18303 40323 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 78 354 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9794081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64625.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.378159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 144 -
Rwork0.216 2649 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: -4.2787 Å / Origin y: 21.2224 Å / Origin z: -26.5256 Å
111213212223313233
T0.0218 Å2-0.0125 Å20.0083 Å2-0.0481 Å2-0.0122 Å2--0.027 Å2
L0.263 °2-0.0186 °2-0.0153 °2-0.7747 °2-0.0418 °2--0.3393 °2
S-0.0067 Å °-0.0439 Å °0.0113 Å °0.0229 Å °-0.0064 Å °-0.1219 Å °0.0118 Å °0.0088 Å °0.0131 Å °

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