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- PDB-3ita: Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. ... -

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Basic information

Entry
Database: PDB / ID: 3ita
TitleCrystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in acyl-enzyme complex with ampicillin
ComponentsD-alanyl-D-alanine carboxypeptidase dacC
KeywordsHYDROLASE / PPenicillin-Binding Protein / BP6 / DD-carboxypeptidase / peptidoglycan / ampicillin / acyl-enzyme complex / Carboxypeptidase / Cell inner membrane / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis / Protease
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to xenobiotic stimulus / protein homodimerization activity ...serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to xenobiotic stimulus / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AIC / Chem-AIX / D-alanyl-D-alanine carboxypeptidase DacC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Crystal structures of penicillin-binding protein 6 from Escherichia coli.
Authors: Chen, Y. / Zhang, W. / Shi, Q. / Hesek, D. / Lee, M. / Mobashery, S. / Shoichet, B.K.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _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 / _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: D-alanyl-D-alanine carboxypeptidase dacC
B: D-alanyl-D-alanine carboxypeptidase dacC
C: D-alanyl-D-alanine carboxypeptidase dacC
D: D-alanyl-D-alanine carboxypeptidase dacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,64212
Polymers152,3654
Non-polymers1,2778
Water13,944774
1
A: D-alanyl-D-alanine carboxypeptidase dacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5393
Polymers38,0911
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanyl-D-alanine carboxypeptidase dacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2833
Polymers38,0911
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanyl-D-alanine carboxypeptidase dacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3794
Polymers38,0911
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanyl-D-alanine carboxypeptidase dacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4412
Polymers38,0911
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.938, 185.980, 83.036
Angle α, β, γ (deg.)90.000, 101.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B
12B
22A
13B
23C

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNILEILEDD187 - 189187 - 189
211ASNASNILEILEBB187 - 189187 - 189
121GLYGLYLYSLYSDD334 - 335334 - 335
221GLYGLYLYSLYSBB334 - 335334 - 335
112GLYGLYLYSLYSBB334 - 335334 - 335
212GLYGLYLYSLYSAA334 - 335334 - 335
113GLYGLYLYSLYSBB334 - 335334 - 335
213GLYGLYLYSLYSCC334 - 335334 - 335

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
D-alanyl-D-alanine carboxypeptidase dacC / DD-carboxypeptidase / DD-peptidase / Penicillin-binding protein 6 / PBP-6


Mass: 38091.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b0839, dacC, JW0823 / Plasmid: PET-24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08506, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID / Ampicillin


Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 292 K / pH: 4.5
Details: PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM Q315R / Detector: CCD / Date: Apr 10, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 148355 / % possible obs: 95 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 19.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.43 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO PBP6 STRUCTURE

Resolution: 1.8→35.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.092 / SU ML: 0.095 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 7305 4.9 %RANDOM
Rwork0.203 ---
obs0.205 148303 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0.47 Å2
2---1.84 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10371 0 78 774 11223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210622
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.97314392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.56351358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19325.171439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.143151850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1411551
X-RAY DIFFRACTIONr_chiral_restr0.1140.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217890
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_it3.1661.56727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.591210802
X-RAY DIFFRACTIONr_scbond_it6.74133895
X-RAY DIFFRACTIONr_scangle_it9.9144.53586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D20tight positional0.430.05
21B8tight positional0.130.05
31B8tight positional0.120.05
12B18loose positional1.795
22A5loose positional1.525
32C5loose positional1.715
11D20tight thermal9.70.5
21B8tight thermal3.70.5
31B8tight thermal1.240.5
12B18loose thermal6.7210
22A5loose thermal1.1710
32C5loose thermal0.9510
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 518 -
Rwork0.371 9733 -
obs--88.51 %

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