[English] 日本語
Yorodumi
- PDB-4z38: Crystal structure of enoyl reductase domain of MlnA from the macr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z38
TitleCrystal structure of enoyl reductase domain of MlnA from the macrolactin biosynthesis cluster from Bacillus amyloliquefaciens
ComponentsMlnA
KeywordsTRANSFERASE / polyketide / pks / enoyl reductase / trans-AT PKS / AT-less / TIM barrel
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / nucleotide binding
Similarity search - Function
PfaD family protein / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / [Acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens subsp. plantarum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJakob, R.P. / Martin, S.F. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MlnA
B: MlnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0584
Polymers106,1452
Non-polymers9132
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-39 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.170, 104.670, 216.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein MlnA


Mass: 53072.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria)
Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: mlnA, RBAM_014330 / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: A7Z470
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG3350, 0.2 M sodium malonate, pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→108.05 Å / Num. obs: 23587 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 95.35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.8
Reflection shellResolution: 2.8→2.92 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6J

2z6j


Resolution: 2.8→108.05 Å / Cor.coef. Fo:Fc: 0.8982 / Cor.coef. Fo:Fc free: 0.8992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1213 5.14 %RANDOM
Rwork0.246 ---
obs0.2469 23587 99.69 %-
Displacement parametersBiso mean: 120.43 Å2
Baniso -1Baniso -2Baniso -3
1-5.3817 Å20 Å20 Å2
2---30.5483 Å20 Å2
3---25.1666 Å2
Refine analyzeLuzzati coordinate error obs: 0.849 Å
Refinement stepCycle: LAST / Resolution: 2.8→108.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13968 0 62 113 14143
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg125681HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3169SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2108HARMONIC5
X-RAY DIFFRACTIONt_it14205HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion924SEMIHARMONIC5
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_contact15053SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3396 145 5.14 %
Rwork0.3038 2677 -
all0.3058 2822 -
obs--99.69 %
Refinement TLS params.

T12: 0.152 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7191-1.4373-1.55930.56160.28272.48970.00950.27990.2273-0.0647-0.0895-0.2140.54420.54420.0799-0.2304-0.09790.304-0.1372-0.304-22.6118-15.559915.3598
24.6695-0.1441-1.43991.1531.49635.96990.19970.37960.5442-0.17780.1448-0.0213-0.4586-0.5442-0.3445-0.3040.0594-0.26810.152-0.2514-48.03720.849434.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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