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- PDB-2xxq: A widespread family of bacterial cell wall assembly proteins -

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Basic information

Entry
Database: PDB / ID: 2xxq
TitleA widespread family of bacterial cell wall assembly proteins
ComponentsCPS2A
KeywordsREPLICATION / PEPTIDOGLYCAN / LCP / LYTR
Function / homology
Function and homology information


DNA replication / membrane
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 / Cps2A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMarles-Wright, J. / Kawai, Y. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Cleverley, R.M. / Bui, N.K. / Ogasawara, N. / Lewis, R.J. ...Marles-Wright, J. / Kawai, Y. / Emmins, R. / Ishikawa, S. / Kuwano, M. / Heinz, N. / Cleverley, R.M. / Bui, N.K. / 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
DepositionNov 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)45,0038
Polymers43,9111
Non-polymers1,0927
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.500, 73.500, 163.790
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: 43911.133 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 98-481 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: D39 / Variant: SEROTYPE 2 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9ZII9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 267 TO ALA

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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: 2.54 Å3/Da / Density % sol: 51.65 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.1 M SODIUM ACETATE PH 4.6, 8 % PEG W/V 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2010 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.77→43.88 Å / Num. obs: 44731 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XXP

2xxp


Resolution: 1.77→37.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.037 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19893 2260 5.1 %RANDOM
Rwork0.17013 ---
obs0.17152 42348 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.338 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 73 374 3333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223017
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9814094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14525.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27115519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.211510
X-RAY DIFFRACTIONr_chiral_restr0.090.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212249
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_it0.651.51881
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21223057
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18431136
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6864.51028
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 176 -
Rwork0.215 3061 -
obs--99.85 %
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)
11.1902-0.37210.91632.8462-1.62343.8617-0.02010.08410.05780.1739-0.1926-0.3388-0.06660.19410.21270.0173-0.0063-0.00830.02050.0330.0643-0.0246-3.217-21.3661
20.6778-0.3993-0.42210.65910.19150.9173-0.0403-0.00180.02610.0070.0271-0.04150.00180.0160.01320.0152-0.01510.00880.0183-0.01370.0236-5.790730.5431-28.5512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A110 - 213
2X-RAY DIFFRACTION2A216 - 482

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