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- PDB-5ty2: Crystal structure of S. aureus penicillin binding protein 4 (PBP4... -

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Basic information

Entry
Database: PDB / ID: 5ty2
TitleCrystal structure of S. aureus penicillin binding protein 4 (PBP4) mutant (E183A, F241R) in complex with nafcillin
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Antibiotic / HYDROLASE / Antibiotic / HYDROLASE - Antibiotic complex
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / beta-lactam antibiotic catabolic process / peptidoglycan biosynthetic process / cell wall organization / beta-lactamase activity / regulation of cell shape / response to antibiotic / proteolysis / membrane
Similarity search - Function
Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A ...Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain / Penicillin-binding protein 4, C-terminal domain superfamily / Domain of unknown function (DUF1958) / 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 / Spermidine Synthase; Chain: A, domain 2 / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-NFF / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and kinetic analysis of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance inStaphylococcus aureus.
Authors: Alexander, J.A.N. / Chatterjee, S.S. / Hamilton, S.M. / Eltis, L.D. / Chambers, H.F. / Strynadka, N.C.J.
History
DepositionNov 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 4
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,59511
Polymers80,4072
Non-polymers1,1899
Water10,971609
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8526
Polymers40,2031
Non-polymers6485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7445
Polymers40,2031
Non-polymers5404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.850, 92.244, 78.952
Angle α, β, γ (deg.)90.000, 98.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-721-

HOH

21B-759-

HOH

DetailsMonomer as determined by size exclusion chromatography

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Penicillin-binding protein 4


Mass: 40203.398 Da / Num. of mol.: 2 / Fragment: residues 25-383 / Mutation: E183A, F241R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0H2WY27

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Non-polymers , 5 types, 618 molecules

#2: Chemical ChemComp-NFF / (2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Nafcillin, bound form / Nafcillin


Mass: 416.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N2O5S / Comment: antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8 mM Zinc chloride, 80 mM sodium acetate pH 5, 100 mM sodium fluoride, and 16% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1046 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1046 Å / Relative weight: 1
ReflectionResolution: 1.7→46.12 Å / Num. obs: 85751 / % possible obs: 96.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Net I/σ(I): 12.9 / Num. measured all: 321983
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.7-1.733.40.8970.621177.9
9-46.123.50.0260.999198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.83 Å46.12 Å
Translation5.83 Å46.12 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.6phasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.7→46.12 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2052 4293 5.01 %
Rwork0.1694 --
obs0.1711 85679 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.85 Å2 / Biso mean: 31.5886 Å2 / Biso min: 13.47 Å2
Refinement stepCycle: final / Resolution: 1.7→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 65 609 6258
Biso mean--35.37 38.28 -
Num. residues----718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075795
X-RAY DIFFRACTIONf_angle_d0.8367880
X-RAY DIFFRACTIONf_chiral_restr0.05896
X-RAY DIFFRACTIONf_plane_restr0.0061011
X-RAY DIFFRACTIONf_dihedral_angle_d10.9573588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.31571060.30062129223576
1.7193-1.73960.31511360.29132299243583
1.7396-1.76080.30831530.28392519267292
1.7608-1.78310.37111280.27092752288097
1.7831-1.80650.3011570.2592681283897
1.8065-1.83130.29771490.24222723287297
1.8313-1.85740.28641360.23382678281497
1.8574-1.88520.24091460.24012753289997
1.8852-1.91460.33461530.25372694284797
1.9146-1.9460.29281490.24722692284197
1.946-1.97960.22561540.19792764291898
1.9796-2.01560.24941480.19022708285698
2.0156-2.05430.24711370.17882737287498
2.0543-2.09630.25251460.18452756290298
2.0963-2.14180.21371200.17352766288698
2.1418-2.19170.20431340.1622747288198
2.1917-2.24650.19621260.17442758288498
2.2465-2.30720.23471580.18372737289598
2.3072-2.37510.22221490.15382767291698
2.3751-2.45180.22261530.1522721287499
2.4518-2.53940.20051380.1522802294099
2.5394-2.6410.22161360.1552790292699
2.641-2.76120.19691460.16072735288199
2.7612-2.90680.2331280.16332829295799
2.9068-3.08890.20371640.16892768293299
3.0889-3.32730.22871360.16442804294099
3.3273-3.6620.17441460.15682812295899
3.662-4.19160.15331530.13552788294199
4.1916-5.27980.13761560.12542824298099
5.2798-46.1390.161520.15882853300599
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)
11.3696-0.8544-0.93251.57910.88992.025-0.02910.042-0.05980.07960.0120.1220.0301-0.11990.02680.1609-0.043-0.0280.17960.0030.169928.5853-48.343840.8896
23.08084.1015-1.67198.142-1.24141.69640.0883-0.145-0.277-0.0401-0.0743-0.50830.0720.2342-0.01940.18070.0054-0.03590.2453-0.02260.195434.6075-71.430620.0723
30.5340.17410.81376.0603-1.21741.7382-0.033-0.00440.03680.10620.13790.446-0.2422-0.1569-0.12150.1623-0.0013-0.00670.2619-0.03580.247225.8393-69.7323.3295
41.66160.72550.22475.71591.02213.20920.08770.0217-0.20240.3276-0.0354-0.21880.4289-0.015-0.05960.1981-0.0029-0.04850.1757-0.01350.187338.0171-67.067535.7889
51.3079-0.2775-0.2141.40410.45832.0034-0.02840.1191-0.1341-0.04590.01380.22290.1683-0.33680.01020.2031-0.0571-0.01980.2098-0.00340.184125.4017-52.36831.7885
64.17771.1456-0.02922.7138-0.13261.24610.03660.42230.5414-0.10380.0257-0.1081-0.24980.1532-0.0720.2164-0.03120.01880.22510.02910.210538.2006-30.354533.6642
70.952-0.2459-0.36821.6810.03650.9705-0.0428-0.09840.05210.36670.0690.15440.0583-0.1396-0.01350.20580.0193-0.00910.18130.01290.146734.3807-46.00721.6339
83.5683.1698-2.4174.7111-1.66081.4692-0.157-0.1758-0.3388-0.4103-0.0917-0.22340.43820.06830.26670.4201-0.00350.0310.23380.02340.231239.7681-69.4462-18.6773
90.4615-0.68710.99425.6106-0.76332.5337-0.11510.0332-0.19-0.11560.1750.58410.3526-0.2491-0.03920.2731-0.04580.02530.26390.00540.263231.5597-67.0997-15.9738
101.21910.54150.115.6920.00912.6189-0.0712-0.0305-0.14090.19210.0129-0.12830.4254-0.0750.03940.26290.0271-0.00920.1880.01320.179543.723-64.7701-3.3482
111.0084-0.2525-0.31392.0929-0.05931.9233-0.00180.0618-0.08950.08250.04230.2710.2-0.298-0.04910.2005-0.0149-0.01080.20710.03080.167531.2371-49.8998-7.4689
124.76563.0656-1.20654.307-1.02721.83910.00580.36830.41960.00680.11850.0759-0.1747-0.0463-0.1440.18850.0480.00720.20190.05270.191338.4093-29.9919-6.3092
136.22042.26530.6383.4491-0.33064.26390.00220.23010.83710.00010.07680.1646-0.17080.1337-0.11460.14570.0107-0.00260.15740.02750.286647.5914-23.6966-5.6797
143.42711.6819-0.45566.7966-1.07354.30990.00510.2206-0.10850.0111-0.0029-0.4952-0.01580.16580.03220.133-0.0056-0.0350.1978-0.01380.242150.6512-31.7478-3.7574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 90 )A25 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 110 )A91 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 137 )A111 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 204 )A138 - 204
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 296 )A205 - 296
6X-RAY DIFFRACTION6chain 'A' and (resid 297 through 383 )A297 - 383
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 90 )B25 - 90
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 111 )B91 - 111
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 137 )B112 - 137
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 204 )B138 - 204
11X-RAY DIFFRACTION11chain 'B' and (resid 205 through 296 )B205 - 296
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 335 )B297 - 335
13X-RAY DIFFRACTION13chain 'B' and (resid 336 through 364 )B336 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 383 )B365 - 383

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