[English] 日本語
Yorodumi
- PDB-3pbk: Structural and Functional Studies of Fatty Acyl-Adenylate Ligases... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pbk
TitleStructural and Functional Studies of Fatty Acyl-Adenylate Ligases from E. coli and L. pneumophila
ComponentsFatty Acyl-Adenylate Ligase
KeywordsLIGASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / FAAL / FATTY ACID AMP LIGASE / ATP-dependent AMP-binding enzyme family
Function / homology
Function and homology information


lipid biosynthetic process / catalytic activity
Similarity search - Function
Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1ZZ / Putative saframycin Mx1 synthetase B / Putative saframycin Mx1 synthetase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and Functional Studies of Fatty Acyl Adenylate Ligases from E. coli and L. pneumophila.
Authors: Zhang, Z. / Zhou, R. / Sauder, J.M. / Tonge, P.J. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
SupersessionFeb 23, 2011ID: 3GQW
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 19, 2012Group: Non-polymer description
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty Acyl-Adenylate Ligase
B: Fatty Acyl-Adenylate Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9894
Polymers129,9302
Non-polymers1,0592
Water1,56787
1
A: Fatty Acyl-Adenylate Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4952
Polymers64,9651
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty Acyl-Adenylate Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4952
Polymers64,9651
Non-polymers5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.469, 118.336, 137.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fatty Acyl-Adenylate Ligase / Putative saframycin Mx1 synthetase B


Mass: 64965.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O6 / Gene: c3712 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Codon+ril Stratagene / References: UniProt: Q8FDN4, UniProt: A0A0H2VDD9*PLUS
#2: Chemical ChemComp-1ZZ / 5'-O-[(S)-(dodecanoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 529.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H36N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M Sodium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→89.824 Å / Num. obs: 30776 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 32.54 Å2 / Rmerge(I) obs: 0.198 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 4 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 3→89.824 Å / SU ML: 0.38 / Isotropic thermal model: Isotropic / σ(F): 0.03 / Phase error: 21.43 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2508 1543 5.07 %
Rwork0.19 --
obs0.193 30439 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2.943 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.3622 Å2-0 Å2-0 Å2
2---3.9783 Å20 Å2
3----5.384 Å2
Refinement stepCycle: LAST / Resolution: 3→89.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8573 0 72 87 8732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088838
X-RAY DIFFRACTIONf_angle_d1.06712009
X-RAY DIFFRACTIONf_dihedral_angle_d19.8173246
X-RAY DIFFRACTIONf_chiral_restr0.0691324
X-RAY DIFFRACTIONf_plane_restr0.0051562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09690.33721360.24442549X-RAY DIFFRACTION98
3.0969-3.20750.31621530.2452542X-RAY DIFFRACTION98
3.2075-3.3360.29211500.23372574X-RAY DIFFRACTION99
3.336-3.48780.29411390.21322598X-RAY DIFFRACTION99
3.4878-3.67170.26891260.19152617X-RAY DIFFRACTION100
3.6717-3.90170.25191370.18552602X-RAY DIFFRACTION99
3.9017-4.2030.20651330.15752630X-RAY DIFFRACTION100
4.203-4.62590.17281280.1392667X-RAY DIFFRACTION100
4.6259-5.29530.21021290.15172661X-RAY DIFFRACTION100
5.2953-6.67120.24031620.18242659X-RAY DIFFRACTION99
6.6712-89.86420.21151500.1742797X-RAY DIFFRACTION99

+
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://pdbjlvh1.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