[English] 日本語
Yorodumi
- PDB-4n1x: Structure of a putative peptidoglycan glycosyltransferase from At... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n1x
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G
ComponentsPeptidoglycan glycosyltransferase
KeywordsTransferase/Antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Susceptibility to Known Mtb Inhibitors / MTBI / glycosyltransferase / penicillin G / Transferase-Antibiotic Complex / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / penicillin binding / cell wall organization / regulation of cell shape / cell division / plasma membrane
Similarity search - Function
: / Penicillin binding protein A dimerisation domain / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain ...: / Penicillin binding protein A dimerisation domain / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan glycosyltransferase
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8184
Polymers99,1452
Non-polymers6732
Water14,412800
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9092
Polymers49,5731
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9092
Polymers49,5731
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.623, 70.141, 115.344
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Peptidoglycan glycosyltransferase


Mass: 49572.531 Da / Num. of mol.: 2 / Fragment: penicillin-binding domain, UNP residues 515-954
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atopobium parvulum (bacteria) / Strain: DSM 20469 / Gene: Apar_1344 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: C8W8H7, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


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


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.085 M MES, 10.2% (w/v) PEG 20000, 10 % (w/v) Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2013 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 70573 / Num. obs: 70573 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 9.2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBF

4jbf


Resolution: 2→29.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.245 / SU ML: 0.122 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23684 3550 5 %RANDOM
Rwork0.19963 ---
obs0.20153 67015 95.92 %-
all-67015 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0 Å21.44 Å2
2---2.88 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5925 0 46 800 6771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196106
X-RAY DIFFRACTIONr_bond_other_d0.0010.025662
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9748333
X-RAY DIFFRACTIONr_angle_other_deg0.888313005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3495824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.824.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84215806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7631522
X-RAY DIFFRACTIONr_chiral_restr0.1130.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4911.2953311
X-RAY DIFFRACTIONr_mcbond_other1.4911.2943310
X-RAY DIFFRACTIONr_mcangle_it2.2611.9334130
X-RAY DIFFRACTIONr_mcangle_other2.2611.9334131
X-RAY DIFFRACTIONr_scbond_it1.91.4772795
X-RAY DIFFRACTIONr_scbond_other1.8971.4762793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7892.1514203
X-RAY DIFFRACTIONr_long_range_B_refined6.9056.937549
X-RAY DIFFRACTIONr_long_range_B_other6.626.4167192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 238 -
Rwork0.223 5090 -
obs--98.68 %
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)
10.9969-0.49940.69974.7052-1.34270.7132-0.20910.14930.10230.5104-0.0061-0.7207-0.22410.09440.21530.1975-0.0315-0.04290.178-0.00090.378720.000235.341249.0876
25.41662.8920.2151.97552.336111.48040.7613-0.9146-0.26090.6092-0.4851-0.18271.10040.0757-0.27610.349-0.1176-0.15990.25860.02780.501933.072844.874664.5766
31.52230.13310.02953.0487-0.90271.40710.0510.11250.0621-0.02710.074-0.3761-0.1550.1517-0.1250.0586-0.00640.03790.0926-0.01740.128812.259823.142444.1107
40.77810.2141-0.25132.3711-0.12460.64960.0150.03920.0902-0.0069-0.00910.13120.0018-0.0319-0.00590.02860.0147-0.02050.06610.00750.038-5.783812.297651.1361
51.3168-0.1588-0.25322.9870.44561.21330.00960.18780.0903-0.30540.0554-0.0297-0.02220.0054-0.0650.08020.0102-0.01290.10820.00370.02490.086813.510238.7317
61.22110.34550.44993.7211-0.36641.0614-0.001-0.0865-0.1393-0.3949-0.0723-0.76310.26650.24720.07330.22890.04490.05120.2040.00940.323226.2184-13.34899.1512
77.0501-9.8733-3.351313.85024.66431.63041.03740.55760.0911-1.4408-0.9121-0.1082-0.5982-0.1535-0.12530.71670.05470.07770.5702-0.02290.641235.7824-19.7973-4.6446
81.4205-0.1050.22343.5371-0.61870.41060.0296-0.1255-0.01680.13220.008-0.24820.08910.1731-0.03760.13010.0298-0.04450.1771-0.02850.109517.21-2.983714.3654
90.5037-0.31540.09821.7363-0.20290.52740.0447-0.0230.0006-0.05980.01290.0402-0.0161-0.0228-0.05750.0891-0.01660.01450.0682-0.00250.0118-0.005110.30145.4781
101.40180.1428-0.14742.9449-0.59111.1579-0.0447-0.22570.03580.27040.0232-0.204-0.00610.06390.02150.1419-0.0092-0.00130.1062-0.03470.02827.0079.042919.0991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 584
2X-RAY DIFFRACTION2A585 - 603
3X-RAY DIFFRACTION3A604 - 655
4X-RAY DIFFRACTION4A656 - 884
5X-RAY DIFFRACTION5A885 - 949
6X-RAY DIFFRACTION6B523 - 580
7X-RAY DIFFRACTION7B581 - 603
8X-RAY DIFFRACTION8B605 - 668
9X-RAY DIFFRACTION9B669 - 880
10X-RAY DIFFRACTION10B881 - 950

+
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