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- PDB-6c39: Apo crystal structure of wild-type S. aureus penicillin binding p... -

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Basic information

Entry
Database: PDB / ID: 6c39
TitleApo crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4)
ComponentsSerine-type D-Ala-D-Ala carboxypeptidaseDD-transpeptidase
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 / membrane => GO:0016020 / 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 / Serine-type D-Ala-D-Ala carboxypeptidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health 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 9, 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 1.2Oct 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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: Serine-type D-Ala-D-Ala carboxypeptidase
B: Serine-type D-Ala-D-Ala carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,76211
Polymers82,1972
Non-polymers5659
Water12,016667
1
A: Serine-type D-Ala-D-Ala carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3485
Polymers41,0981
Non-polymers2504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine-type D-Ala-D-Ala carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4146
Polymers41,0981
Non-polymers3155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.358, 92.403, 79.230
Angle α, β, γ (deg.)90.000, 99.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

ZN

21B-763-

HOH

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Components

#1: Protein Serine-type D-Ala-D-Ala carboxypeptidase / DD-transpeptidase


Mass: 41098.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: HMPREF3211_00659 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL31 / References: UniProt: A0A133Q5K3, UniProt: A0A0H2WY27*PLUS
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
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: 1.69→46.202 Å / Num. obs: 91624 / % possible obs: 99.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.69-1.723.10.97245180.5370.6441.1799.7
9.26-46.230.0355510.9970.0230.04294.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.89 Å46.2 Å
Translation5.89 Å46.2 Å

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Processing

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

1tvf


Resolution: 1.69→46.202 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7
RfactorNum. reflection% reflection
Rfree0.1961 4604 5.03 %
Rwork0.1613 --
obs0.163 91580 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.57 Å2 / Biso mean: 30.6691 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.69→46.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5656 0 17 667 6340
Biso mean--45.81 37.84 -
Num. residues----718
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 (%)
1.69-1.70920.32961580.29442839299799
1.7092-1.72930.26841500.273929303080100
1.7293-1.75040.30261680.254528703038100
1.7504-1.77260.2781760.247828913067100
1.7726-1.79590.31211400.242829013041100
1.7959-1.82050.26511610.22928923053100
1.8205-1.84650.26421640.211329353099100
1.8465-1.87410.23111380.211828883026100
1.8741-1.90340.24621650.197729133078100
1.9034-1.93460.22481720.185628803052100
1.9346-1.96790.23461620.18229113073100
1.9679-2.00370.19751460.17529013047100
2.0037-2.04220.2261620.171128813043100
2.0422-2.08390.22471470.15929513098100
2.0839-2.12920.16751420.15429483090100
2.1292-2.17880.19021440.152129233067100
2.1788-2.23330.17241400.143529073047100
2.2333-2.29360.18071450.144229263071100
2.2936-2.36110.18261510.149829193070100
2.3611-2.43730.17281730.14742874304799
2.4373-2.52440.19451510.148729163067100
2.5244-2.62550.22691470.149829363083100
2.6255-2.7450.20411510.1512946309799
2.745-2.88970.17951310.14912898302999
2.8897-3.07070.19791640.15872888305299
3.0707-3.30770.21061450.1582874301998
3.3077-3.64050.18241470.14362865301297
3.6405-4.1670.12371610.13032860302197
4.167-5.24880.15251450.12742858300396
5.2488-46.21880.2091580.17382855301395
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)
11.12490.355-0.27911.6512-0.31310.7925-0.0181-0.012-0.0208-0.04380.028-0.1068-0.01330.1118-0.00120.12470.0039-0.01640.15330.00170.13222.8076-47.1951-1.9389
21.5952-2.1792-0.1566.50220.33941.38890.00560.1721-0.0775-0.0032-0.0196-0.0187-0.055-0.1070.00510.12870.0022-0.01440.19110.02420.126521.6863-69.376716.5451
31.7495-1.20490.64175.5314-1.3512.43430.0228-0.0327-0.1725-0.24010.05490.33360.2055-0.0107-0.07790.1399-0.0239-0.02030.13840.02330.163213.6282-65.86332.6329
40.73970.0920.36571.7256-0.79241.34860.0083-0.1214-0.06740.09-0.0358-0.17160.06080.13410.02860.12420.0042-0.01150.14980.01560.142225.7219-51.27397.0484
53.8027-0.9841-0.38222.43180.77891.7293-0.0255-0.32310.51550.0736-0.01320.1316-0.2655-0.1795-0.01910.1888-0.0009-0.00690.1598-0.01450.180412.589-29.09965.4227
63.3332.7186-0.33182.5340.22664.1911-0.1070.468-0.2138-0.47160.2013-0.35230.10740.2272-0.0970.28480.0150.03410.13880.02040.174536.408-39.0217-45.8267
70.2931-0.0898-0.11691.1653-0.06280.4182-0.05510.0201-0.0084-0.10250.05330.0880.1476-0.026-0.00330.2171-0.0238-0.01230.1846-0.0030.156423.2075-55.7566-30.5641
82.3161-0.34280.2373.50540.3023.4183-0.05050.0502-0.09920.02120.0633-0.03510.38920.1148-0.00990.2185-0.0011-0.00090.12320.00820.113827.8432-65.2196-24.8969
91.7492-1.11930.49895.9661-1.16231.0307-0.03240.1116-0.0429-0.5320.05370.20050.21960.0113-0.02150.2994-0.0636-0.05730.1672-0.00380.137218.8202-62.2109-38.7794
101.8036-0.31390.5591.4703-0.94281.58490.0532-0.1163-0.0624-0.1732-0.0176-0.03130.22280.079-0.02620.1608-0.00570.00280.1192-0.00860.103831.2792-49.6229-28.4288
112.30010.09570.35396.23281.1712.94270.06640.1898-0.1374-0.5919-0.0981-0.34570.16690.0455-0.01180.2001-0.00150.02130.12130.03680.102632.9971-45.9905-37.8342
126.1132-4.1764-2.50334.8112.05031.87680.1547-0.13210.3211-0.1298-0.03730.0188-0.1317-0.0499-0.11170.1896-0.02860.00050.1525-0.01110.148324.1474-27.8206-32.3931
136.5658-1.9663-0.78253.0674-0.37345.91880.0683-0.03230.5865-0.0272-0.0362-0.0911-0.2336-0.2277-0.0530.1416-0.0135-0.0210.1084-0.02350.236915.607-21.9022-33.4873
141.9479-1.2461-1.17978.02221.79735.93460.0654-0.0954-0.06480.0309-0.17750.50450.1046-0.36510.29810.0631-0.0198-0.07340.19410.01010.257312.1046-29.8242-35.1514
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 137 )A91 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 204 )A138 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 296 )A205 - 296
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 383 )A297 - 383
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 56 )B25 - 56
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 111 )B57 - 111
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 154 )B112 - 154
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 204 )B155 - 204
10X-RAY DIFFRACTION10chain 'B' and (resid 205 through 266 )B205 - 266
11X-RAY DIFFRACTION11chain 'B' and (resid 267 through 296 )B267 - 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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