[English] 日本語
Yorodumi
- PDB-5tw8: Crystal structure of wild-type S. aureus penicillin binding prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tw8
TitleCrystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftaroline
ComponentsPenicillin-binding protein 4
KeywordsHYDROLASE / Antibiotic / Hydrolase / Penicillin binding protein / beta-lactam antibiotics / 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
Ceftaroline, bound form / Penicillin-binding protein 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 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 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 11, 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 1.2Oct 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_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,0039
Polymers80,5032
Non-polymers1,5007
Water8,665481
1
A: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0555
Polymers40,2511
Non-polymers8044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9484
Polymers40,2511
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.415, 92.165, 79.153
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
11B-402-

ZN

21B-700-

HOH

DetailsMonomer as determined by size exclusion chromatography

-
Components

#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 (strain COL) (bacteria)
Strain: COL / Gene: pbp4, SACOL0699 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0H2WY27
#2: Chemical ChemComp-AI8 / Ceftaroline, bound form


Mass: 607.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N8O5S4
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.75 %
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

-
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: 1.72→46.08 Å / Num. obs: 87247 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.066 / Rrim(I) all: 0.128 / Net I/σ(I): 7.8 / Num. measured all: 327221
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.72-1.753.81.4130.612199.7
9.26-46.083.50.0410.996198.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.94 Å46.08 Å
Translation5.94 Å46.08 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX`refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVF

1tvf


Resolution: 1.72→46.08 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2146 4378 5.02 %
Rwork0.1862 --
obs0.1876 87188 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 33.3412 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.72→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 83 481 6159
Biso mean--79.98 38.45 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065826
X-RAY DIFFRACTIONf_angle_d0.8567908
X-RAY DIFFRACTIONf_chiral_restr0.048888
X-RAY DIFFRACTIONf_plane_restr0.0051025
X-RAY DIFFRACTIONf_dihedral_angle_d12.6153624
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 (%)
1.72-1.73950.34881410.349326962837100
1.7395-1.760.35681640.338327432907100
1.76-1.78150.3691510.318527332884100
1.7815-1.8040.32951540.307627732927100
1.804-1.82780.30881410.301327252866100
1.8278-1.85280.28231460.276127792925100
1.8528-1.87930.31681480.269927292877100
1.8793-1.90730.31841530.27827632916100
1.9073-1.93710.35631590.329627052864100
1.9371-1.96890.25091490.234927602909100
1.9689-2.00280.22131400.227627592899100
2.0028-2.03930.24731560.212627472903100
2.0393-2.07850.26131390.208627792918100
2.0785-2.12090.24821320.19827842916100
2.1209-2.1670.18951360.185627632899100
2.167-2.21740.21261400.188527362876100
2.2174-2.27290.2941350.241727892924100
2.2729-2.33430.23711430.190527522895100
2.3343-2.4030.2171530.175827712924100
2.403-2.48060.17561550.164527872942100
2.4806-2.56920.21611360.167427362872100
2.5692-2.67210.24061300.170527732903100
2.6721-2.79370.21841490.17627482897100
2.7937-2.9410.20741300.17127962926100
2.941-3.12520.20191550.16872749290499
3.1252-3.36640.21021380.167127762914100
3.3664-3.70510.19851470.148527862933100
3.7051-4.24090.141540.132827642918100
4.2409-5.34180.14311510.134827982949100
5.3418-46.0990.19441530.17412811296499
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)
10.9272-0.7216-0.54962.58450.76531.8072-0.01170.0992-0.0725-0.00860.0010.21250.0011-0.1794-0.00350.0596-0.0174-0.02220.14610.00230.111929.0386-47.022340.9974
22.14722.54041.66058.2074-0.12772.86470.0067-0.1133-0.0647-0.10460.04160.0505-0.04680.0046-0.07290.16650.0029-0.01730.2002-0.050.138831.3933-68.717523.4786
31.0527-0.3906-0.00823.69260.56741.3160.00920.1142-0.1358-0.0240.02480.23810.0808-0.1855-0.03050.1575-0.0423-0.00290.1958-0.01620.141630.944-55.95734.1818
44.1291.3351-0.92753.4897-1.23912.7580.09530.46070.5894-0.0324-0.0262-0.1134-0.36980.1674-0.04350.25280.00280.00070.17750.03440.186938.9966-29.277633.7657
52.8173-3.17-0.68664.354-0.57076.1376-0.1576-0.5504-0.20140.70350.36140.69650.1227-0.2897-0.08730.36380.0640.08490.179-0.01310.22928.1022-39.03176.8865
60.6203-0.0943-0.18972.0280.53311.063-0.1388-0.0808-0.04340.17070.109-0.04390.296-0.05490.01170.26380.0426-0.01040.17170.01080.12941.2661-55.8146-8.8979
72.79180.02832.43184.8716-0.51223.0031-0.091-0.1493-0.16760.09820.2120.29590.4842-0.3088-0.07870.3613-0.03340.04460.20260.00830.149236.3172-65.069-14.3513
82.39411.48710.88067.82910.67123.6446-0.0488-0.186-0.13420.73020.0399-0.20520.4279-0.06610.04330.34540.1002-0.03190.1920.00360.144945.5753-62.2987-0.36
94.31651.12361.38683.34851.25283.4196-0.12170.2460.0377-0.04910.1330.10040.2073-0.0443-0.02120.23240.05280.00070.11260.01150.111636.7474-50.2732-13.0183
106.2531-3.4474.02785.7952-4.68238.5703-0.08-0.0395-0.06230.01130.24130.34590.4712-0.5509-0.18880.2693-0.02020.03340.1505-0.02090.149727.3535-48.2471-7.03
113.74290.08571.12325.8021-1.1255.4085-0.0216-0.2605-0.16460.50880.14390.50520.401-0.2592-0.07680.19870.05340.05190.1169-0.01730.141731.3753-45.593-1.4007
127.75036.4059-3.54477.7165-3.45193.1437-0.06870.25160.2989-0.0020.08270.026-0.02710.0746-0.05660.17130.0617-0.04150.17640.03050.172540.289-27.843-6.5713
136.3042.9871-1.66625.77270.31718.06460.0610.06920.4857-0.1665-0.04520.2799-0.38510.2886-0.10420.18320.0028-0.06540.12110.00430.256549.0321-22.2259-5.5832
143.82031.4452-1.42017.001-1.59887.41620.03740.2535-0.1057-0.0483-0.1058-0.60160.16770.44470.06830.08380.0464-0.07360.2262-0.04510.277352.2689-29.881-3.9489
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 382 )A297 - 382
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 239 )B205 - 239
10X-RAY DIFFRACTION10chain 'B' and (resid 240 through 266 )B240 - 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more