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- PDB-5txi: Crystal structure of wild-type S. aureus penicillin binding prote... -

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Basic information

Entry
Database: PDB / ID: 5txi
TitleCrystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftobiprole
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 / metal ion binding / 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-RB6 / Penicillin-binding protein 4 / Penicillin-binding protein 4, putative
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _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.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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)82,28517
Polymers80,5032
Non-polymers1,78215
Water10,449580
1
A: Penicillin binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1629
Polymers40,2511
Non-polymers9108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1238
Polymers40,2511
Non-polymers8727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.904, 92.293, 79.519
Angle α, β, γ (deg.)90.000, 100.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Penicillin binding protein 4


Mass: 40251.414 Da / Num. of mol.: 2 / Fragment: residues 25-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0H2WY27, UniProt: Q2G2X6*PLUS

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Non-polymers , 7 types, 595 molecules

#2: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N8O6S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8 mM Zinc chloride, 80 mM sodium acetate pH 5, 400 mM Dimethyl (2-hydroxyethyl) ammonium propane sulfonate, and 16% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→46.15 Å / Num. obs: 107535 / % possible obs: 98.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.045 / Rrim(I) all: 0.075 / Net I/σ(I): 8.5 / Num. measured all: 271517
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.6-1.632.20.8040.544189.4
8.76-46.152.50.0270.997196

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.89 Å46.15 Å
Translation5.89 Å46.15 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data 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: 1.6→46.147 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.78
RfactorNum. reflection% reflection
Rfree0.2024 5439 5.06 %
Rwork0.171 --
obs0.1726 107471 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.23 Å2 / Biso mean: 24.2653 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.6→46.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 98 580 6299
Biso mean--35.75 33.59 -
Num. residues----718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155898
X-RAY DIFFRACTIONf_angle_d1.4168014
X-RAY DIFFRACTIONf_chiral_restr0.088899
X-RAY DIFFRACTIONf_plane_restr0.0091039
X-RAY DIFFRACTIONf_dihedral_angle_d12.2213673
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 (%)
1.6-1.61820.31071730.30813060323388
1.6182-1.63720.31651710.29743183335494
1.6372-1.65720.32941920.2763446363899
1.6572-1.67820.2941840.2643406359099
1.6782-1.70030.28051930.26123389358299
1.7003-1.72350.28551780.2483430360899
1.7235-1.74820.27051800.23173460364099
1.7482-1.77430.28292050.23153425363099
1.7743-1.8020.23471910.217834003591100
1.802-1.83150.26481770.213234303607100
1.8315-1.86310.2291760.194934383614100
1.8631-1.8970.22621860.192834733659100
1.897-1.93350.21762060.176134263632100
1.9335-1.9730.2141910.171234133604100
1.973-2.01590.18941800.167234773657100
2.0159-2.06270.21761830.159534383621100
2.0627-2.11430.20881730.16023442361599
2.1143-2.17150.2021600.16473433359399
2.1715-2.23540.21761760.15813434361099
2.2354-2.30750.19621740.16043466364099
2.3075-2.390.19231840.15893426361099
2.39-2.48570.19121860.16113440362699
2.4857-2.59880.21751680.16393390355898
2.5988-2.73580.20391730.17153427360098
2.7358-2.90720.21671650.17793414357998
2.9072-3.13160.19861870.16843391357897
3.1316-3.44670.20181780.16433364354297
3.4467-3.94520.15851730.14123375354896
3.9452-4.96960.1411890.12983363355296
4.9696-46.16570.16881870.15093373356095
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)
11.2953-1.2472-1.16124.3430.08253.87590.0153-0.079-0.13010.29160.06210.4749-0.0486-0.2306-0.0650.123-0.0025-0.00370.1449-0.00020.146121.355-41.802546.2331
2-0.0102-0.01150.09411.66921.01630.7525-0.01110.0224-0.0105-0.04980.0527-0.10330.01840.0057-0.05050.1147-0.0153-0.01410.1467-0.01060.111634.529-58.421631.3037
30.41210.68690.94174.50520.61291.8736-0.0037-0.04390.03870.18990.02010.1304-0.028-0.0372-0.0130.174-0.01080.01410.1699-0.03430.105229.4676-68.338925.0181
42.041.27530.98666.41062.2523.31280.0721-0.0445-0.17160.5151-0.0264-0.29560.315-0.1097-0.04550.13990.0066-0.050.145-0.00910.147838.7208-65.2639.2607
51.4352-0.32620.26362.15090.77091.7897-0.00870.1361-0.1408-0.0739-0.03230.18880.087-0.21340.02910.1111-0.0159-0.01450.1341-0.01680.11825.9172-51.259331.8343
64.00411.7718-0.67433.0812-0.84361.6961-0.00030.32340.4569-0.06270.0297-0.0537-0.19230.1366-0.04030.15220.0079-0.01740.16490.00970.140638.8346-29.500633.5287
72.1343-1.8404-0.77013.2051-0.5573.5505-0.125-0.2902-0.13850.43440.19970.36220.073-0.1917-0.06610.20380.00080.02180.130.00150.119928.1392-39.20166.6625
80.2523-0.1363-0.08521.75240.24560.8311-0.0317-0.0169-0.01660.03510.0161-0.09230.19570.0140.00990.13260.0056-0.01960.1370.01250.100241.6427-55.9594-8.6975
90.02480.17950.01255.4883-2.18351.1321-0.0663-0.0023-0.0613-0.06120.18370.33520.233-0.114-0.11590.1935-0.0177-0.03090.1721-0.00450.156333.0601-65.5596-15.7882
104.15370.78571.22374.44540.59934.2219-0.0597-0.0081-0.1010.11030.0095-0.18280.33170.09880.04940.13850.0312-0.01860.09380.02460.093846.1366-60.7604-5.2808
110.53151.99911.18867.48754.5594.19440.1104-0.163-0.14590.7879-0.18860.03690.4951-0.16540.0680.2319-0.0038-0.00490.15670.03270.160242.6372-66.90991.836
120.9932-0.11940.12021.94730.38951.3251-0.01520.0056-0.04990.0885-0.00010.13910.1437-0.13150.00740.0956-0.0047-0.0060.11180.00920.082632.8285-48.5709-7.5035
134.67492.2307-1.14522.8195-0.55351.44430.08790.12840.5364-0.00120.0290.0808-0.10670.1462-0.11050.11550.0333-0.01540.13770.02630.138743.8861-25.9291-6.3348
142.81970.7281-0.94835.1747-0.9754.65190.07660.164-0.1548-0.0208-0.0761-0.32540.06020.31670.04260.04580.01-0.05460.1576-0.02350.173252.5271-29.9947-4.0028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 56 )A25 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 111 )A57 - 111
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 154 )A112 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 204 )A155 - 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 56 )B25 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 111 )B57 - 111
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 137 )B112 - 137
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 183 )B138 - 183
11X-RAY DIFFRACTION11chain 'B' and (resid 184 through 204 )B184 - 204
12X-RAY DIFFRACTION12chain 'B' and (resid 205 through 296 )B205 - 296
13X-RAY DIFFRACTION13chain 'B' and (resid 297 through 364 )B297 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 383 )B365 - 383

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