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- PDB-6c3k: Apo crystal structure of S. aureus penicillin binding protein 4 (... -

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Basic information

Entry
Database: PDB / ID: 6c3k
TitleApo crystal structure of S. aureus penicillin binding protein 4 (PBP4) mutant (E183A, F241R)
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Penicillin binding protein
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 / metal ion binding
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
Penicillin-binding protein 4
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 analyses 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
DepositionJan 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.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)82,54511
Polymers82,1012
Non-polymers4449
Water12,917717
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3056
Polymers41,0501
Non-polymers2555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2405
Polymers41,0501
Non-polymers1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.868, 92.561, 79.189
Angle α, β, γ (deg.)90.000, 99.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin-binding protein 4


Mass: 41050.332 Da / Num. of mol.: 2 / Mutation: E183A, F241R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0H2WY27
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
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: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→46.28 Å / Num. obs: 108799 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.037 / Rrim(I) all: 0.068 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.631.14954270.4410.7561.38199.8
8.76-46.280.0226860.9980.0140.02698.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.17data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.6→46.28 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.204 5499 5.07 %
Rwork0.1759 --
obs0.1773 108546 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.71 Å2 / Biso mean: 32.7827 Å2 / Biso min: 11.33 Å2
Refinement stepCycle: final / Resolution: 1.6→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 9 717 6356
Biso mean--27.74 38.51 -
Num. residues----716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.29991880.306734473635100
1.6182-1.63720.32561980.303334133611100
1.6372-1.65720.30981930.295834723665100
1.6572-1.67820.28041820.272334313613100
1.6782-1.70030.29421850.265234433628100
1.7003-1.72350.25841860.259834733659100
1.7235-1.74820.27331870.238234243611100
1.7482-1.77430.22832090.224434533662100
1.7743-1.8020.27681720.214934203592100
1.802-1.83150.23081890.205334503639100
1.8315-1.86310.21321810.197334683649100
1.8631-1.8970.29471870.22923401358899
1.897-1.93350.40591940.35923269346395
1.9335-1.97290.25241910.211634493640100
1.9729-2.01580.21631820.178834493631100
2.0158-2.06270.20921880.178534273615100
2.0627-2.11430.23271740.21133339351397
2.1143-2.17150.19251590.159434673626100
2.1715-2.23540.20651660.16633416358299
2.2354-2.30750.25581670.21743304347194
2.3075-2.390.17321850.156234653650100
2.39-2.48570.17181910.148434853676100
2.4857-2.59880.20771780.151134203598100
2.5988-2.73580.22271770.16163461363899
2.7358-2.90720.20351640.157334963660100
2.9072-3.13160.17471910.157334493640100
3.1316-3.44670.18871810.163454363599
3.4467-3.94520.15251750.13863464363999
3.9452-4.96960.13761950.12443441363699
4.9696-46.29980.18291840.1633497368198
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)
11.4348-0.2423-0.47241.66720.43421.3112-0.01590.0119-0.04870.0379-0.00610.1789-0.0059-0.13340.03760.1024-0.0039-0.02180.13960.00110.123229.0986-48.111341.0128
21.95471.57361.86076.09720.20071.9523-0.011-0.1914-0.05130.00160.13470.0795-0.0473-0.0105-0.1590.1484-0.00080.02060.2018-0.05140.142531.5535-69.930823.6774
30.8723-0.11060.01851.89610.4860.6849-0.00470.1275-0.101-0.0041-0.00740.11640.0634-0.0562-0.00060.1308-0.0119-0.00690.1413-0.02570.13530.6972-57.10834.4342
43.6090.6091-0.31022.2133-0.72531.6360.02930.32890.5607-0.0664-0.0474-0.0906-0.20570.1556-0.02190.17820.0118-0.00650.16360.02790.198139.1297-30.163133.7972
52.7766-2.9328-0.06653.7488-0.24025.9014-0.0581-0.5254-0.28310.35870.22450.49470.191-0.35-0.1340.2381-0.02620.04740.157-0.00730.18328.1752-39.97886.7085
60.48170.0635-0.06021.55770.3080.4756-0.0512-0.0459-0.03750.16340.0544-0.07420.148-0.02320.00230.17410.0186-0.00340.15440.00970.11341.3995-56.7085-8.5324
72.3074-0.04310.64183.6881-0.26063.3912-0.0465-0.0878-0.1876-0.03020.09390.11720.4452-0.1832-0.03330.2201-0.01920.01310.1389-0.00650.118936.7787-66.1543-14.2334
81.71411.09720.18945.21160.69151.0248-0.0107-0.0982-0.10510.5261-0.0042-0.29380.19980.02590.03050.26460.0404-0.04940.16260.0150.122345.8445-63.1197-0.3488
91.5192-0.00630.32381.48190.77831.76160.02480.1004-0.00860.1246-0.02310.0980.2146-0.1618-0.01090.1515-0.01320.00290.1320.01320.110233.3032-50.5214-10.6268
102.76940.6151-0.24296.8111-2.3144.33970.0258-0.1476-0.05460.3727-0.02250.3190.2007-0.1272-0.0090.14450.00260.01610.1088-0.02570.08532.1746-46.0047-2.3708
115.47722.4199-1.17752.1426-0.29141.06350.08010.13920.6710.05440.04680.1564-0.11690.053-0.1260.1820.0311-0.01820.1610.02250.218443.8509-26.4467-6.0363
121.05331.5046-0.70497.887-1.7814.8121-0.02870.0597-0.1557-0.0139-0.1414-0.520.09890.30850.26370.05760.0186-0.0680.1774-0.0030.215252.5542-30.9689-3.7239
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 154 )A91 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 296 )A155 - 296
4X-RAY DIFFRACTION4chain 'A' and (resid 297 through 383 )A297 - 383
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 56 )B25 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 111 )B57 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 154 )B112 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 204 )B155 - 204
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 266 )B205 - 266
10X-RAY DIFFRACTION10chain 'B' and (resid 267 through 296 )B267 - 296
11X-RAY DIFFRACTION11chain 'B' and (resid 297 through 364 )B297 - 364
12X-RAY DIFFRACTION12chain 'B' and (resid 365 through 383 )B365 - 383

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