[English] 日本語
Yorodumi
- PDB-7o4b: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o4b
TitleCrystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase
Function / homology
Function and homology information


penicillin binding / membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
CITRIC ACID / OPEN FORM - PENICILLIN G / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus , an essential component of the divisome machinery.
Authors: Martinez-Caballero, S. / Mahasenan, K.V. / Kim, C. / Molina, R. / Feltzer, R. / Lee, M. / Bouley, R. / Hesek, D. / Fisher, J.F. / Munoz, I.G. / Chang, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionApr 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 1, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_database_status.pdb_format_compatible / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 1
C: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,02218
Polymers144,7162
Non-polymers2,30616
Water70339
1
A: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5599
Polymers72,3581
Non-polymers1,2018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4639
Polymers72,3581
Non-polymers1,1058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.649, 180.649, 223.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111AAA64 - 589
2111BBB64 - 589

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Penicillin-binding protein 1


Mass: 72358.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin


Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.593→47.513 Å / Num. obs: 45182 / % possible obs: 96.3 % / Redundancy: 24.7 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.03 / Net I/σ(I): 22.1
Reflection shellResolution: 2.593→2.846 Å / Rmerge(I) obs: 2.163 / Num. unique obs: 2260 / Rpim(I) all: 0.42

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRO

5tro


Resolution: 2.593→47.505 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.331 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.515 / ESU R Free: 0.312
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2415 2318 5.13 %
Rwork0.2048 42863 -
all0.207 --
obs-45181 67.427 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.084 Å2-0.042 Å2-0 Å2
2---0.084 Å20 Å2
3---0.273 Å2
Refinement stepCycle: LAST / Resolution: 2.593→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7755 0 94 39 7888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177556
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.65110778
X-RAY DIFFRACTIONr_angle_other_deg1.2081.59217482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97823.817393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.416151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2987
X-RAY DIFFRACTIONr_chiral_restr_other0.1420.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021799
X-RAY DIFFRACTIONr_nbd_refined0.2070.21494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26936
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.215
X-RAY DIFFRACTIONr_nbd_other0.2150.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4270.21
X-RAY DIFFRACTIONr_mcbond_it5.6736.4283922
X-RAY DIFFRACTIONr_mcbond_other5.6646.4273921
X-RAY DIFFRACTIONr_mcangle_it8.6239.6344892
X-RAY DIFFRACTIONr_mcangle_other8.6239.6364893
X-RAY DIFFRACTIONr_scbond_it5.8666.894079
X-RAY DIFFRACTIONr_scbond_other5.8256.8754066
X-RAY DIFFRACTIONr_scangle_it9.04310.1025886
X-RAY DIFFRACTIONr_scangle_other9.01910.0855869
X-RAY DIFFRACTIONr_lrange_it11.95772.4338485
X-RAY DIFFRACTIONr_lrange_other11.9672.4448486
X-RAY DIFFRACTIONr_ncsr_local_group_10.1140.0514842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114160.05008
12CX-RAY DIFFRACTIONLocal ncs0.114160.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.593-2.660.528180.3682890.37548860.7210.8256.28330.353
2.66-2.7330.371250.3686410.36847150.7720.80114.12510.345
2.733-2.8120.47510.3518090.35746100.7340.79518.65510.323
2.812-2.8980.337500.3311160.3344760.7640.79326.050.291
2.898-2.9930.357920.32216430.32443510.770.78539.87590.282
2.993-3.0970.3021140.31820990.31742180.8070.78752.46560.283
3.097-3.2140.2941460.28227240.28240680.8680.85970.55060.243
3.214-3.3440.291960.26134710.26339510.8640.88992.8120.225
3.344-3.4920.2611760.22735980.22837740.9050.9131000.191
3.492-3.6620.2531930.20534140.20836070.9120.9291000.171
3.662-3.8590.2491820.18732690.1934510.9250.9421000.163
3.859-4.0910.2031740.16431020.16532760.9470.9571000.14
4.091-4.3710.1891560.15529240.15630800.9620.9661000.136
4.371-4.7180.1741530.1427360.14228890.9660.9721000.126
4.718-5.1630.2141350.15925440.16226790.9560.9661000.145
5.163-5.7640.2281110.17723250.1824370.9490.9699.9590.163
5.764-6.640.271070.19720780.20121850.9360.9491000.186
6.64-8.0930.211970.20617680.20718650.9380.9391000.199
8.093-11.2820.255910.21814230.22115140.9390.9461000.222
11.282-47.5050.301510.3258900.3239410.8570.8821000.332

+
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