[English] 日本語
Yorodumi
- PDB-4g4v: Crystal structure of peptidoglycan-associated lipoprotein from Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g4v
TitleCrystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii
ComponentsPeptidoglycan-associated lipoprotein
KeywordsPEPTIDE BINDING PROTEIN / OmpA-like domain / MEMBRANE PROTEIN
Function / homologyOmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / 2,6-DIAMINOPIMELIC ACID / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, W.C. / Song, J.H. / Park, J.S. / Kim, H.Y.
CitationJournal: To be Published
Title: Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA
Authors: Lee, W.C. / Park, J.S. / Song, J.H. / Kim, S.I. / Lee, J.C. / Cheong, J. / Kim, H.Y.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0042
Polymers12,8141
Non-polymers1901
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 45.130, 50.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peptidoglycan-associated lipoprotein


Mass: 12814.040 Da / Num. of mol.: 1 / Fragment: UNP residues 75-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: TCDC-AB0715 / Gene: pal / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0QP95, UniProt: A0A7U3YVT1*PLUS
#2: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID / Diaminopimelic acid


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.85 Å3/Da / Density % sol: 33.63 % / Mosaicity: 1.278 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 0.1M PHOSPHATE CITRATE, 30% PEG 3350, pH 4.2, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 7884 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Χ2: 3.123 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.976.90.3277671.941100
1.97-2.056.90.267752.2461100
2.05-2.146.90.1897692.506199.9
2.14-2.256.70.1617792.7921100
2.25-2.396.70.1367753.086199.9
2.39-2.586.70.1077743.435199.9
2.58-2.846.50.0927873.532199.7
2.84-3.256.30.0667933.649199.9
3.25-4.095.90.0578094.116199.8
4.09-505.50.0548564.264198.4

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TD4

3td4


Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2618 415 5.2 %
Rwork0.2258 --
obs-7850 99.1 %
Solvent computationBsol: 39.427 Å2
Displacement parametersBiso max: 62.46 Å2 / Biso mean: 33.1362 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 13 50 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.209
X-RAY DIFFRACTIONc_mcbond_it1.4281.5
X-RAY DIFFRACTIONc_scbond_it2.2592
X-RAY DIFFRACTIONc_mcangle_it2.1132
X-RAY DIFFRACTIONc_scangle_it3.2932.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.3675380.257468071893.5
1.97-2.050.2375340.2499749783100
2.05-2.140.2723360.236573477099.9
2.14-2.250.2829500.2346731781100
2.25-2.390.2771300.244575378399.9
2.39-2.580.2549410.228673677799.9
2.58-2.840.3519370.237375579299.7
2.84-3.250.2544450.242574879399.9
3.25-4.090.2773550.217575380899.8
4.09-500.2154490.204879684598.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6API.paramAPI.top

+
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