[English] 日本語
Yorodumi
- PDB-6tm4: NatL2 in complex with two molecules of salicylic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tm4
TitleNatL2 in complex with two molecules of salicylic acid
Components(PaaK-like ligase (AMP-dependent synthetase and ...) x 2
KeywordsLIGASE / phenyl acetate CoA ligase
Function / homologyANL, N-terminal domain / ligase activity / AMP-dependent synthetase/ligase / AMP-binding enzyme / nucleotide binding / metal ion binding / ADENOSINE MONOPHOSPHATE / 2-HYDROXYBENZOIC ACID / AMP-dependent synthetase and ligase
Function and homology information
Biological speciesStreptomyces sp. Tu 6176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsNaismith, J.H. / Song, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility.
Authors: Song, H. / Rao, C. / Deng, Z. / Yu, Y. / Naismith, J.H.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: PaaK-like ligase (AMP-dependent synthetase and ligase)
BBB: PaaK-like ligase (AMP-dependent synthetase and ligase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,73011
Polymers96,6502
Non-polymers1,0799
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-40 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.460, 139.240, 129.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11BBB-661-

HOH

21BBB-692-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

-
Components

-
PaaK-like ligase (AMP-dependent synthetase and ... , 2 types, 2 molecules AAABBB

#1: Protein PaaK-like ligase (AMP-dependent synthetase and ligase) / Coenzyme F390 synthetase


Mass: 48289.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A022MRT4
#2: Protein PaaK-like ligase (AMP-dependent synthetase and ligase) / Coenzyme F390 synthetase


Mass: 48360.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A022MRT4

-
Non-polymers , 5 types, 169 molecules

#3: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M KSCN, 0.1 M sodium citrate pH 6, 24-32% PEG MME 2K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.89→71.13 Å / Num. obs: 77807 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.4
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5703 / CC1/2: 0.65 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SIW

6siw


Resolution: 1.89→71.128 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.202 / SU B: 10.773 / SU ML: 0.143 / Average fsc free: 0.8366 / Average fsc work: 0.8455 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2303 3811 4.9 %
Rwork0.1978 73962 -
all0.199 --
obs-77773 99.949 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.313 Å2
Baniso -1Baniso -2Baniso -3
1--2.732 Å20 Å20 Å2
2--3.626 Å20 Å2
3----0.894 Å2
Refinement stepCycle: LAST / Resolution: 1.89→71.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 67 160 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136958
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176440
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6669490
X-RAY DIFFRACTIONr_angle_other_deg1.3061.57314836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43719.742388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.626151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4461577
X-RAY DIFFRACTIONr_chiral_restr0.0670.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021585
X-RAY DIFFRACTIONr_nbd_refined0.1930.21270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.26053
X-RAY DIFFRACTIONr_nbtor_refined0.1610.23316
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2260
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.217
X-RAY DIFFRACTIONr_nbd_other0.2180.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.28
X-RAY DIFFRACTIONr_mcbond_it1.7952.8313444
X-RAY DIFFRACTIONr_mcbond_other1.7922.833443
X-RAY DIFFRACTIONr_mcangle_it2.7344.2364298
X-RAY DIFFRACTIONr_mcangle_other2.7344.2374299
X-RAY DIFFRACTIONr_scbond_it2.1963.083514
X-RAY DIFFRACTIONr_scbond_other2.1953.083513
X-RAY DIFFRACTIONr_scangle_it3.4784.5185192
X-RAY DIFFRACTIONr_scangle_other3.4784.5185193
X-RAY DIFFRACTIONr_lrange_it5.32232.4627546
X-RAY DIFFRACTIONr_lrange_other5.32332.4067529
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0512963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.89-1.9390.3752720.34854260.3556990.4150.44999.98250.328
1.939-1.9920.3142910.32852520.32755450.5530.51799.96390.305
1.992-2.050.2982840.29151240.29154090.7650.75399.98150.263
2.05-2.1130.2832380.26450190.26552570.8310.8271000.235
2.113-2.1820.2972820.24747900.2550750.8430.85799.94090.22
2.182-2.2590.2682270.22647230.22749510.8650.88999.97980.2
2.259-2.3440.252230.2145230.21247470.9060.91799.97890.187
2.344-2.4390.2532460.20743650.20946120.9170.92199.97830.186
2.439-2.5480.2611990.20141680.20343700.9180.93499.93140.18
2.548-2.6720.2242380.20240000.20342410.930.93599.92930.184
2.672-2.8160.2452030.19837880.239910.9190.9381000.186
2.816-2.9870.2471850.20536300.20738170.9220.93499.94760.201
2.987-3.1930.2511560.21334340.21535910.9210.93399.97220.211
3.193-3.4480.2141400.231830.20133270.9450.95299.87980.206
3.448-3.7760.2271590.18629360.18830950.9410.9551000.198
3.776-4.220.21420.16526670.16728130.9590.96599.85780.19
4.22-4.870.178990.14823970.14924970.9690.97499.960.178
4.87-5.9580.206960.16820150.16921140.9580.96699.85810.203
5.958-8.3960.169860.15715850.15716750.970.97199.76120.196
8.396-71.1280.183450.1769370.1779860.9750.9799.59430.229
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)
11.1214-0.20070.42870.8580.41772.34420.0694-0.3842-0.43820.11730.0919-0.00880.5452-0.177-0.16130.1326-0.0412-0.03670.15670.1670.2021-31.2548-24.1558-13.5355
22.1166-0.59060.03120.74720.1171.3540.02710.11350.0442-0.2015-0.0113-0.0723-0.10310.1079-0.01580.1206-0.0313-0.01740.02730.01070.0391-26.1609-8.9329-42.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA*4 - 601
2X-RAY DIFFRACTION2ALLB*0 - 801

+
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