[English] 日本語
Yorodumi
- PDB-4z37: Structure of the ketosynthase of module 2 of C0ZGQ5 (trans-AT PKS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z37
TitleStructure of the ketosynthase of module 2 of C0ZGQ5 (trans-AT PKS) from Brevibacillus brevis
ComponentsPutative mixed polyketide synthase/non-ribosomal peptide synthetase
KeywordsTRANSFERASE / polyketide / ketosynthase / trans-AT / AT-less / pks
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / : / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Thiolase/Chalcone synthase / Putative AMP-binding domain signature. / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative mixed polyketide synthase/non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsMartin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: The structural organization of trans-AT polyketide synthases: ketoacyl synthase and trans-acting enoyl reductase
Authors: Martin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)72,2551
Polymers72,2551
Non-polymers00
Water7,927440
1
A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase

A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)144,5102
Polymers144,5102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4750 Å2
ΔGint-27 kcal/mol
Surface area44380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.292, 85.800, 89.254
Angle α, β, γ (deg.)90.00, 121.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3435-

HOH

-
Components

#1: Protein Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Mass: 72254.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria)
Strain: 47 / JCM 6285 / NBRC 100599 / Gene: BBR47_39870 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: C0ZGQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 % / Description: rod like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium malonate, pH 7, and 15% polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→42.9 Å / Num. obs: 49103 / % possible obs: 99.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9
Reflection shellResolution: 1.998→2.05 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.5 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 1.998→42.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 2476 5.04 %
Rwork0.1732 --
obs0.1749 49103 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 0 440 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044944
X-RAY DIFFRACTIONf_angle_d0.7966704
X-RAY DIFFRACTIONf_dihedral_angle_d13.381840
X-RAY DIFFRACTIONf_chiral_restr0.037713
X-RAY DIFFRACTIONf_plane_restr0.003879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9979-2.03630.25051360.2662471X-RAY DIFFRACTION95
2.0363-2.07790.31631200.25882559X-RAY DIFFRACTION99
2.0779-2.1230.30061460.25062538X-RAY DIFFRACTION100
2.123-2.17240.26831270.24182631X-RAY DIFFRACTION99
2.1724-2.22680.23931290.22042602X-RAY DIFFRACTION100
2.2268-2.2870.26371370.20852599X-RAY DIFFRACTION100
2.287-2.35430.21571420.19572573X-RAY DIFFRACTION100
2.3543-2.43020.23911480.18972585X-RAY DIFFRACTION100
2.4302-2.51710.26221620.18172586X-RAY DIFFRACTION100
2.5171-2.61790.22741490.1862558X-RAY DIFFRACTION100
2.6179-2.7370.2361430.16912627X-RAY DIFFRACTION100
2.737-2.88120.21421330.17312601X-RAY DIFFRACTION100
2.8812-3.06170.22351460.17312591X-RAY DIFFRACTION100
3.0617-3.2980.19051220.16492593X-RAY DIFFRACTION100
3.298-3.62980.21091260.15722616X-RAY DIFFRACTION100
3.6298-4.15460.17081310.14532630X-RAY DIFFRACTION100
4.1546-5.23290.15641470.13462609X-RAY DIFFRACTION99
5.2329-42.90990.18511320.17112658X-RAY DIFFRACTION99
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)
13.19591.5981.19342.18110.98771.7789-0.06410.18060.4427-0.3111-0.09780.2131-0.19320.04160.14920.22170.0306-0.03670.2180.0620.26235.269148.2142-16.754
22.36530.0220.59863.06950.20462.03940.08990.02230.0165-0.0372-0.04220.12370.0235-0.1812-0.05760.12970.016-0.00720.22450.03050.1797-7.387440.0422-11.1119
32.51030.04840.42481.4482-0.10471.44460.05860.00490.108-0.0456-0.04510.0419-0.0247-0.0624-0.020.1680.0244-0.02530.1660.00940.18263.90140.9751-8.8378
42.2077-0.30330.68711.85660.26612.30830.1298-0.006-0.27610.0798-0.0265-0.17530.28980.1399-0.12990.18860.0304-0.02140.2130.0150.293114.446828.7619-3.7394
53.2602-0.18331.50681.0483-0.13721.9050.16570.5862-0.2954-0.2804-0.0532-0.18240.28870.4143-0.07130.26410.08180.03330.2957-0.05170.243114.815530.5915-20.6877
65.0991.28970.59962.6866-0.09722.3457-0.05790.7910.0188-0.7650.20660.41670.0696-0.1637-0.15990.56330.05-0.18820.5484-0.03210.3501-19.016833.8094-39.6544
75.00591.27331.93683.50141.07284.1727-0.09330.6585-0.2663-0.3269-0.0470.37750.1312-0.02610.12050.29720.0574-0.01760.3706-0.02770.2391-12.60934.0466-31.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2318 through 2426 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2427 through 2461 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2462 through 2577 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2578 through 2618 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2619 through 2819 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2820 through 2885 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2886 through 2933 )

+
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