[English] 日本語
Yorodumi
- PDB-4lcl: Simvastatin Synthase (LOVD), from Aspergillus Terreus, LovD6 muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lcl
TitleSimvastatin Synthase (LOVD), from Aspergillus Terreus, LovD6 mutant (simh6208)
ComponentsTransesterase
KeywordsTRANSFERASE / laboratory-directed evolution / Transesterase
Function / homology
Function and homology information


monacolin J acid methylbutanoate transferase / lovastatin biosynthetic process / polyketide synthase activity / polyketide biosynthetic process / acyltransferase activity / antibiotic biosynthetic process / defense response to fungus / hydrolase activity
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGao, X. / Sawaya, M.R. / Yeates, T.O. / Tang, Y.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: The role of distant mutations and allosteric regulation on LovD active site dynamics.
Authors: Jimenez-Oses, G. / Osuna, S. / Gao, X. / Sawaya, M.R. / Gilson, L. / Collier, S.J. / Huisman, G.W. / Yeates, T.O. / Tang, Y. / Houk, K.N.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Jun 4, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Transesterase
B: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9084
Polymers96,7882
Non-polymers1202
Water6,900383
1
A: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4542
Polymers48,3941
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4542
Polymers48,3941
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 76.390, 113.760
Angle α, β, γ (deg.)90.000, 93.910, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are two biological units in the asymmetric unit (chain A and chain B).

-
Components

#1: Protein Transesterase


Mass: 48394.133 Da / Num. of mol.: 2
Mutation: A9V K26E C40A N43R C60N A123P M157V S164G S172N A178L N191G L192I Q241M A247S R250K G275S Q297E L361M V370I A383V H404K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: lovD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y7D1
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% PEG-4000, 50mM sodium citrate pH 5.6, 16% propanol, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9641 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 1.8→18.1 Å / Num. all: 69030 / Num. obs: 69030 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.45 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.01
Reflection shell
Resolution (Å)Mean I/σ(I) obsRsym valueDiffraction-ID% possible allNum. unique all
1.8-1.853.1751.5199.5
3.29-3.650.492.1199.1
3.6-4.6552.552199
4.65-5.6954.141.7199.3
5.69-8.0553.961.8199.3
8.05-18.157.271.6195.6787

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.55 Å
Translation3 Å45.55 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLC

3hlc


Resolution: 1.8→18.1 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9471 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3448 5 %RANDOM
Rwork0.1672 ---
obs0.1684 68966 99.48 %-
all-68966 --
Displacement parametersBiso max: 123.68 Å2 / Biso mean: 28.0407 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.8964 Å20 Å20.2552 Å2
2---1.1644 Å20 Å2
3---2.0608 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 8 383 6741
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2319SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes964HARMONIC5
X-RAY DIFFRACTIONt_it6541HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion817SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8121SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6541HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8860HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion15.51
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2168 255 5.01 %
Rwork0.1977 4834 -
all0.1986 5089 -
obs--99.48 %
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)
10.7766-0.1055-0.00310.7517-0.16580.96150.010.12420.0214-0.09940.01320.0188-0.0083-0.0388-0.0231-0.05880.00870.0035-0.06210.0053-0.058516.53524.486411.3501
21.2158-0.1173-0.09221.1346-0.37161.33790.0374-0.3267-0.00450.13670.03830.0349-0.0160.0081-0.0757-0.1178-0.00860.0043-0.05-0.0043-0.111612.552554.757244.9126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-10 - 413
2X-RAY DIFFRACTION2{ B|* }B-9 - 413

+
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