[English] 日本語
Yorodumi
- PDB-5ja2: EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ja2
TitleEntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the non-Native MbtH-Like Protein PA2412
Components
  • Enterobactin synthase component F
  • MbtH-Like Protein PA2412
KeywordsLIGASE / NONRIBOSOMAL PEPTIDE SYNTHETASE / NRPS / CONDENSATION / ADENYLATION / PCP / THIOESTERASE / MBTH-LIKE PROTEIN / PHOSPHOPANTETHEINE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / pyoverdine biosynthetic process / enterobactin synthetase complex / enterobactin biosynthetic process / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity ...L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / pyoverdine biosynthetic process / enterobactin synthetase complex / enterobactin biosynthetic process / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol Acetyltransferase / Condensation domain ...MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-75C / Meso-2,3-Butanediol / Enterobactin synthase component F / MbtH-like domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiller, B.R. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture.
Authors: Miller, B.R. / Drake, E.J. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
#1: Journal: Nature / Year: 2016
Title: Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.
Authors: Drake, E.J. / Miller, B.R. / Shi, C. / Tarrasch, J.T. / Sundlov, J.A. / Allen, C.L. / Skiniotis, G. / Aldrich, C.C. / Gulick, A.M.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enterobactin synthase component F
B: MbtH-Like Protein PA2412
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,9175
Polymers150,9632
Non-polymers9543
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area53470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.270, 57.690, 182.424
Angle α, β, γ (deg.)90.00, 97.62, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Enterobactin synthase component F / Enterochelin synthase F / Serine-activating enzyme / Seryl-AMP ligase


Mass: 142313.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: entF, b0586, JW0578 / Variant: W3110 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein MbtH-Like Protein PA2412


Mass: 8649.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2412 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I169
#3: Chemical ChemComp-75C / 5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine


Mass: 773.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H44N9O13PS2
#4: Chemical ChemComp-BU9 / Meso-2,3-Butanediol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.98 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Bis Tris propane, 50-150 mM MgCl2, and 15-28% Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 113.15 K / Ambient temp details: Liquid Nitrogen Gas Stream
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→58.98 Å / Num. obs: 31728 / % possible obs: 94.88 % / Redundancy: 3.1 % / Biso Wilson estimate: 65.6 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.1026 / Net I/σ(I): 6.66
Reflection shellResolution: 3→3.107 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.6214 / Mean I/σ(I) obs: 1.37 / % possible all: 90.53

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JA1

5ja1


Resolution: 3→58.974 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1529 4.82 %
Rwork0.2047 --
obs0.2065 31728 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→58.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9791 0 61 15 9867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210130
X-RAY DIFFRACTIONf_angle_d0.54713887
X-RAY DIFFRACTIONf_dihedral_angle_d10.7546009
X-RAY DIFFRACTIONf_chiral_restr0.041603
X-RAY DIFFRACTIONf_plane_restr0.0051814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.0970.32041370.29272565X-RAY DIFFRACTION90
3.097-3.20770.34521390.26452788X-RAY DIFFRACTION96
3.2077-3.33610.26211530.25922770X-RAY DIFFRACTION98
3.3361-3.48790.30531370.24782737X-RAY DIFFRACTION96
3.4879-3.67180.23261300.21972765X-RAY DIFFRACTION95
3.6718-3.90180.25481170.20782643X-RAY DIFFRACTION92
3.9018-4.2030.24061350.18912804X-RAY DIFFRACTION97
4.203-4.62580.22541380.17342769X-RAY DIFFRACTION96
4.6258-5.29480.20821450.17142738X-RAY DIFFRACTION93
5.2948-6.66940.22361420.21622803X-RAY DIFFRACTION97
6.6694-58.98510.21941560.18042817X-RAY DIFFRACTION93
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)
14.8684-3.1108-0.15224.24631.18111.93360.12740.17530.19890.19380.0379-0.42850.05030.4039-0.16510.7336-0.0229-0.07220.31260.0110.4182-46.810211.738732.5641
22.43821.23351.41943.75431.38991.8328-0.03680.34760.1520.26930.0564-0.08630.04570.2465-0.01490.62790.07080.06580.36330.0060.3321-51.4275-13.862222.082
38.75035.20251.93555.71194.61745.0263-0.3991-0.13710.1586-0.0294-0.1082-0.01690.6307-0.16540.45410.5726-0.0010.02070.3438-0.01310.2643-71.1711-22.86857.2878
42.59850.61920.40361.05690.75583.056-0.04430.0201-0.0394-0.19620.1415-0.09440.04580.1647-0.09470.5353-0.02710.10990.20230.02870.3241-64.9346-29.395-25.0721
58.8091-2.9152.01274.3579-1.19864.2444-0.119-0.21130.20830.17160.1433-0.3735-0.0620.7416-0.06380.5190.02560.09620.5125-0.1340.4003-36.0239-28.9019-16.8894
61.6911.63560.99026.0166-1.69692.13640.36091.72880.9878-0.5337-0.393-1.02580.78351.5967-0.09520.9207-0.01560.28341.20580.22350.8504-36.7108-15.9413-36.6
73.85230.8998-1.94273.9428-0.2726.5207-0.57611.42870.2023-1.11310.7014-0.0850.7645-0.9386-0.16541.041-0.38820.07751.22890.05990.492-62.4274-23.2146-68.5552
83.61412.23920.8867.44720.19547.99990.535-0.9765-0.83090.6098-0.5974-0.68451.09390.4835-0.04040.77280.06510.02290.76580.38110.678-61.5986-46.3104-1.5276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:186 )A18 - 186
2X-RAY DIFFRACTION2( CHAIN A AND RESID 187:429 )A187 - 429
3X-RAY DIFFRACTION3( CHAIN A AND RESID 430:444 )A430 - 444
4X-RAY DIFFRACTION4( CHAIN A AND RESID 445:857 )A445 - 857
5X-RAY DIFFRACTION5( CHAIN A AND RESID 858:963 )A858 - 963
6X-RAY DIFFRACTION6( CHAIN A AND RESID 971:1043 )A971 - 1043
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1052:1292 )A1052 - 1292
8X-RAY DIFFRACTION8( CHAIN B AND RESID 0:67 )B0 - 67

+
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