[English] 日本語
Yorodumi
- PDB-4gr4: Crystal structure of SlgN1deltaAsub -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gr4
TitleCrystal structure of SlgN1deltaAsub
ComponentsNon-ribosomal peptide synthetase
KeywordsLIGASE / MbtH-like domain / adenylation domain / Rossmann fold / ATP Binding
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphiryn-III C-methyltransferase, conserved site / ANL, N-terminal domain / Amino acid adenylation domain ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphiryn-III C-methyltransferase, conserved site / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces lydicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsHerbst, D.A. / Zocher, G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis of the Interaction of MbtH-like Proteins, Putative Regulators of Nonribosomal Peptide Biosynthesis, with Adenylating Enzymes.
Authors: Herbst, D.A. / Boll, B. / Zocher, G. / Stehle, T. / Heide, L.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-ribosomal peptide synthetase
B: Non-ribosomal peptide synthetase
C: Non-ribosomal peptide synthetase
D: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,9215
Polymers196,8854
Non-polymers351
Water7,963442
1
A: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2572
Polymers49,2211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.110, 148.610, 109.580
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Non-ribosomal peptide synthetase


Mass: 49221.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lydicus (bacteria) / Gene: slgN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ybdz- / References: UniProt: D1GLU5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100 mM Tris-HCl, 0.2 M Li2SO4, 1.3 M K/Na tartrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.44→47.65 Å / Num. all: 96463 / Num. obs: 95771 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.35 Å2
Reflection shellResolution: 2.44→2.5 Å / Mean I/σ(I) obs: 1.84 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→35.72 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.9111 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 4790 5 %RANDOM
Rwork0.1804 ---
obs0.1821 95737 99.63 %-
all-96463 --
Displacement parametersBiso mean: 43.52 Å2
Baniso -1Baniso -2Baniso -3
1--5.3825 Å20 Å23.8221 Å2
2--3.5906 Å20 Å2
3---1.7919 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2.44→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13340 0 1 442 13783
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113663HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1718629HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4387SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2107HARMONIC5
X-RAY DIFFRACTIONt_it13663HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion19.18
X-RAY DIFFRACTIONt_chiral_improper_torsion1696SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15256SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2672 325 4.68 %
Rwork0.2208 6614 -
all0.223 6939 -
obs--99.63 %
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)
10.81920.00490.28811.19710.3611.3177-0.0001-0.1321-0.02310.1312-0.0469-0.01080.1111-0.12820.047-0.1185-0.0381-0.0183-0.06190.0078-0.0885-15.306423.1979-26.3067
21.0051-0.08550.0861.28660.17751.30420.0246-0.11970.02580.2422-0.09160.0589-0.0122-0.06310.067-0.0416-0.0320.0309-0.1280.0107-0.12132.2468-19.7637-16.0791
30.97480.31540.20021.4520.27691.49420.01490.1944-0.0167-0.17330.04910.05050.13670.0236-0.0639-0.07410.0179-0.0377-0.10930.016-0.1281-40.743512.6377-75.2446
41.1926-0.0289-0.53631.52450.07371.6786-0.00040.1626-0.0258-0.2210.00790.093-0.0637-0.1287-0.0075-0.15690.0305-0.023-0.0909-0.0063-0.1141-57.6053-31.2568-63.3344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 466
2X-RAY DIFFRACTION2B0 - 466
3X-RAY DIFFRACTION3C3 - 465
4X-RAY DIFFRACTION4D2 - 466

+
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