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- PDB-4cjn: Crystal structure of PBP2a from MRSA in complex with quinazolinon... -

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Basic information

Entry
Database: PDB / ID: 4cjn
TitleCrystal structure of PBP2a from MRSA in complex with quinazolinone ligand
ComponentsPENICILLIN BINDING PROTEIN 2 PRIME
KeywordsHYDROLASE / IMMUNE SYSTEM / ALLOSTERIC SITE
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / membrane => GO:0016020 / response to antibiotic / membrane
Similarity search - Function
NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / beta-muramic acid / Chem-QNZ / Penicillin binding protein 2 prime / Penicillin binding protein 2 prime
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 Å
AuthorsBouley, R. / Otero, L.H. / Rojas-Altuve, A. / Hermoso, J.A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2015
Title: Discovery of Antibiotic (E)-3-(3-Carboxyphenyl)-2-(4-Cyanostyryl)Quinazolin-4(3H)-One.
Authors: Bouley, R. / Kumarasiri, M. / Peng, Z. / Otero, L.H. / Song, W. / Suckow, M.A. / Schroeder, V.A. / Wolter, W.R. / Lastochkin, E. / Antunes, N.T. / Pi, H. / Vakulenko, S. / Hermoso, J.A. / ...Authors: Bouley, R. / Kumarasiri, M. / Peng, Z. / Otero, L.H. / Song, W. / Suckow, M.A. / Schroeder, V.A. / Wolter, W.R. / Lastochkin, E. / Antunes, N.T. / Pi, H. / Vakulenko, S. / Hermoso, J.A. / Chang, M. / Mobashery, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: How Allosteric Control of Staphylococcus Aureus Penicillin Binding Protein 2A Enables Methicillin Resistance and Physiological Function.
Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / ...Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / Chang, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionDec 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN BINDING PROTEIN 2 PRIME
B: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,06113
Polymers146,5732
Non-polymers1,48711
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-66.7 kcal/mol
Surface area58140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.050, 103.773, 186.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein PENICILLIN BINDING PROTEIN 2 PRIME / PENICILLIN-BINDING PROTEIN 2A


Mass: 73286.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: Q54113, UniProt: A0A0J9X1X5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#4: Sugar ChemComp-MUR / beta-muramic acid / muramic acid / Muramic acid


Type: D-saccharide, beta linking / Mass: 251.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO7
IdentifierTypeProgram
b-D-GlcpN3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 304 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-QNZ / (E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl)benzoic acid


Mass: 393.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H15N3O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 % / Description: NONE
Crystal growpH: 7 / Details: PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.95→63.96 Å / Num. obs: 115623 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 25.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 18.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZG0

3zg0


Resolution: 1.947→63.876 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 5767 5 %
Rwork0.1985 --
obs0.2009 115133 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.947→63.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 72 295 10669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810541
X-RAY DIFFRACTIONf_angle_d1.07414180
X-RAY DIFFRACTIONf_dihedral_angle_d12.8254075
X-RAY DIFFRACTIONf_chiral_restr0.0481534
X-RAY DIFFRACTIONf_plane_restr0.0051860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9465-1.96860.43181580.36373417X-RAY DIFFRACTION93
1.9686-1.99180.40491840.343601X-RAY DIFFRACTION99
1.9918-2.01610.36152300.30763542X-RAY DIFFRACTION99
2.0161-2.04160.36371780.29083607X-RAY DIFFRACTION100
2.0416-2.06850.3121850.27563602X-RAY DIFFRACTION99
2.0685-2.09680.34872000.27473601X-RAY DIFFRACTION99
2.0968-2.12680.33371970.26583624X-RAY DIFFRACTION99
2.1268-2.15850.33491840.25053601X-RAY DIFFRACTION100
2.1585-2.19230.27241830.24043628X-RAY DIFFRACTION99
2.1923-2.22820.27811970.22383575X-RAY DIFFRACTION99
2.2282-2.26660.3062070.22013621X-RAY DIFFRACTION100
2.2666-2.30780.3092130.22733609X-RAY DIFFRACTION100
2.3078-2.35220.34192050.23093591X-RAY DIFFRACTION100
2.3522-2.40020.2731650.23073643X-RAY DIFFRACTION100
2.4002-2.45240.28722130.22383615X-RAY DIFFRACTION100
2.4524-2.50950.30231850.21753627X-RAY DIFFRACTION100
2.5095-2.57220.2591810.21413646X-RAY DIFFRACTION100
2.5722-2.64180.26391810.21413658X-RAY DIFFRACTION100
2.6418-2.71950.26571720.21483656X-RAY DIFFRACTION100
2.7195-2.80730.28641970.23873669X-RAY DIFFRACTION100
2.8073-2.90760.30161730.24443678X-RAY DIFFRACTION100
2.9076-3.02410.28151910.24513636X-RAY DIFFRACTION100
3.0241-3.16170.28712010.2413687X-RAY DIFFRACTION100
3.1617-3.32840.28871810.23483688X-RAY DIFFRACTION100
3.3284-3.53690.26781990.20813682X-RAY DIFFRACTION100
3.5369-3.80990.21371960.18093696X-RAY DIFFRACTION100
3.8099-4.19330.19961810.15473728X-RAY DIFFRACTION100
4.1933-4.79990.1782020.13433729X-RAY DIFFRACTION100
4.7999-6.04660.20872100.15793773X-RAY DIFFRACTION100
6.0466-63.91050.20142180.17023936X-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)
11.14560.30490.23481.9086-0.41721.38760.07420.4161-0.0931-0.35060.05270.08190.26120.396100.6805-0.1153-0.11060.6989-0.0320.55695.8951-26.3402-92.0358
20.75010.0614-0.18260.2681-0.14372.5719-0.1235-0.035-0.1046-0.03520.0005-0.05240.87640.4785-0.05990.58340.16180.0160.29580.02650.428323.024-23.1578-33.7329
30.3406-0.06190.00951.709-0.21983.3212-0.0702-0.35940.16940.1846-0.0377-0.0820.14370.0253-0.02430.41140.06080.00750.39760.03590.409416.519-16.4345-14.877
41.59980.6070.50120.73290.25872.73950.02840.1877-0.0171-0.24280.0704-0.0214-0.54140.83590.00730.5504-0.12910.07310.5426-0.0070.455231.0363-0.2304-84.0527
50.5761-0.2001-0.71110.05730.24720.86780.12910.3899-0.1376-0.2072-0.009-0.01090.0149-0.75170.00120.57140.0098-0.06420.8685-0.0170.519-11.2348-12.8489-70.2478
62.37-0.3919-2.05320.38650.58552.25150.1677-0.08210.1376-0.0122-0.03750.0512-0.2674-0.21350.00450.41480.0465-0.01060.55350.07010.4727-17.0976-1.2009-36.4582
70.9495-0.247-0.83280.2143-0.01441.0606-0.2677-0.509-0.45360.199-0.06890.36260.4826-0.3271-0.09480.6018-0.02840.07830.89450.16540.766-24.9293-13.8577-26.6309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 27 THROUGH 147 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 148 THROUGH 539 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 540 THROUGH 668 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 27 THROUGH 147 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 148 THROUGH 242 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 243 THROUGH 564 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 565 THROUGH 668 )

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