[English] 日本語
Yorodumi
- PDB-3p3e: Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p3e
TitleCrystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LIPID A BIOSYNTHESIS / LIPID A SYNTHESIS / LPXC / baab sandwich / Deacetylation / ANTIBIOTIC / Acyl UDP-GlcNac / HYDROXAMATE / LPC-009
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3P3 / NITRATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsLee, C.-J. / Zhou, P.
CitationJournal: Chem.Biol. / Year: 2011
Title: Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design.
Authors: Lee, C.J. / Liang, X. / Chen, X. / Zeng, D. / Joo, S.H. / Chung, H.S. / Barb, A.W. / Swanson, S.M. / Nicholas, R.A. / Li, Y. / Toone, E.J. / Raetz, C.R. / Zhou, P.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,21330
Polymers33,1471
Non-polymers2,06629
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.637, 73.608, 88.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase / Protein envA


Mass: 33146.617 Da / Num. of mol.: 1 / Fragment: UNP residues 1-299 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: envA, lpxC, PA4406 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

-
Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3P3 / N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide


Mass: 362.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate trihydrate pH 5.0, and 2.7 M ammonium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 88611 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.28-1.34.10.45694.9
1.3-1.335.10.439100
1.33-1.355.50.391100
1.35-1.385.80.355100
1.38-1.4160.324100
1.41-1.4460.276100
1.44-1.4860.24100
1.48-1.526.10.211100
1.52-1.566.10.181100
1.56-1.616.10.161100
1.61-1.676.10.147100
1.67-1.746.10.136100
1.74-1.826.10.126100
1.82-1.916.10.119100
1.91-2.036.10.114100
2.03-2.196.20.118100
2.19-2.416.20.126100
2.41-2.766.20.111100
2.76-3.476.10.104100
3.47-505.70.10298.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.1 Å
Translation2.5 Å26.1 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→22.99 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 4429 5.02 %
Rwork0.182 --
obs0.182 88305 99.5 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.09 Å2 / ksol: 0.47 e/Å3
Displacement parametersBiso mean: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.2614 Å2-0 Å2-0 Å2
2---0.0819 Å2-0 Å2
3----0.1795 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 130 413 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092593
X-RAY DIFFRACTIONf_angle_d0.8573496
X-RAY DIFFRACTIONf_dihedral_angle_d11.988947
X-RAY DIFFRACTIONf_chiral_restr0.051383
X-RAY DIFFRACTIONf_plane_restr0.004473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.32680.25714070.25078143X-RAY DIFFRACTION98
1.3268-1.37990.23774220.22348340X-RAY DIFFRACTION100
1.3799-1.44270.22614470.20388305X-RAY DIFFRACTION100
1.4427-1.51870.20814320.19328327X-RAY DIFFRACTION100
1.5187-1.61390.20194140.18168375X-RAY DIFFRACTION100
1.6139-1.73840.19024560.18358363X-RAY DIFFRACTION100
1.7384-1.91330.18814790.17668346X-RAY DIFFRACTION100
1.9133-2.190.17944550.16698417X-RAY DIFFRACTION100
2.19-2.75840.19594480.1798528X-RAY DIFFRACTION100
2.7584-22.99150.1854690.1788732X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.4203 Å / Origin y: 3.9916 Å / Origin z: -7.8744 Å
111213212223313233
T0.0682 Å20.0063 Å2-0.0004 Å2-0.0806 Å2-0.0008 Å2--0.0819 Å2
L0.4192 °2-0.0545 °20.2016 °2-0.5059 °20.2002 °2--0.6718 °2
S0.0121 Å °0.0227 Å °-0.0067 Å °-0.0041 Å °0.029 Å °0.0095 Å °0.0303 Å °0.0317 Å °-0.036 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID ALL

+
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