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- PDB-4q6z: LpoB C-terminal domain from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4q6z
TitleLpoB C-terminal domain from Escherichia coli
ComponentsPenicillin-binding protein activator LpoB
KeywordsPROTEIN BINDING / mixed alpha-beta / Lipoprotein / Activator of PBP1b / PBP1b / lipidation / outer-membrane
Function / homology
Function and homology information


periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / regulation of cell shape
Similarity search - Function
Penicillin-binding protein activator LpoB / Peptidoglycan-synthase activator LpoB / ABC-type transport auxiliary lipoprotein component / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein activator LpoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into the Lipoprotein Outer Membrane Regulator of Penicillin-binding Protein 1B.
Authors: King, D.T. / Lameignere, E. / Strynadka, N.C.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein activator LpoB
B: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)28,4702
Polymers28,4702
Non-polymers00
Water43224
1
A: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)14,2351
Polymers14,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)14,2351
Polymers14,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-2 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.930, 96.930, 96.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 78 - 212 / Label seq-ID: 1 - 135

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Penicillin-binding protein activator LpoB / PBP activator LpoB


Mass: 14235.036 Da / Num. of mol.: 2 / Fragment: LpoB C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: lpoB, UTI89_C1233 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RD49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris, 2M ammonium sulfate , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→68.54 Å / Num. all: 7758 / Num. obs: 7727 / % possible obs: 99.6 %
Reflection shellResolution: 2.8→2.95 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERMRphasing
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→68.54 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.966 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28859 355 4.6 %RANDOM
Rwork0.22531 ---
obs0.22828 7350 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.961 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 24 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191992
X-RAY DIFFRACTIONr_bond_other_d0.0060.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9512698
X-RAY DIFFRACTIONr_angle_other_deg1.06534432
X-RAY DIFFRACTIONr_chiral_restr0.0640.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02444
X-RAY DIFFRACTIONr_mcbond_it3.6856.0841078
X-RAY DIFFRACTIONr_mcbond_other3.6866.0821077
X-RAY DIFFRACTIONr_mcangle_it5.9679.1181344
X-RAY DIFFRACTIONr_mcangle_other5.9659.121345
X-RAY DIFFRACTIONr_scbond_it3.9586.488914
X-RAY DIFFRACTIONr_scbond_other3.9566.49915
X-RAY DIFFRACTIONr_scangle_other6.5989.5591355
X-RAY DIFFRACTIONr_long_range_B_refined10.16561.391588
X-RAY DIFFRACTIONr_long_range_B_other10.16361.41589
Refine LS restraints NCS

Ens-ID: 1 / Number: 6604 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.22 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 25 -
Rwork0.314 537 -
obs--100 %

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