[English] 日本語
Yorodumi
- PDB-4bko: Enoyl-ACP reducatase FabV from Burkholderia pseudomallei (apo) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bko
TitleEnoyl-ACP reducatase FabV from Burkholderia pseudomallei (apo)
ComponentsPUTATIVE REDUCTASE BURPS305_1051
KeywordsOXIDOREDUCTASE / FAS-II / MELIOIDOSIS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHirschbeck, M.W. / Neckles, C. / Tonge, P.J. / Kisker, C.
CitationJournal: To be Published
Title: Point Mutation Changes Substrate Binding Mechanism and Inhibitor Specificity of Yersinia Pestis Enoyl- Acp Reductase Fabv
Authors: Neckles, C. / Hirschbeck, M.W. / Shah, S. / Pan, P. / Bommineni, G.R. / Yu, W. / Liu, N. / Davoodi, S. / Kisker, C. / Tonge, P.J.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE REDUCTASE BURPS305_1051
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,02010
Polymers44,9691
Non-polymers1,0519
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.640, 93.320, 100.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PUTATIVE REDUCTASE BURPS305_1051 / ENOYL-ACP REDUCTASE


Mass: 44968.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: BP82 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4MGI8, UniProt: A0A0E1S3N2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCBI REFERENCE SEQUENCE ZP_01769530.1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.67 % / Description: NONE
Crystal growDetails: 2 M AMMONIUM SULFATE, 100 MM MES PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→35.01 Å / Num. obs: 36997 / % possible obs: 100 % / Observed criterion σ(I): 5.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZU3

3zu3


Resolution: 1.9→35.009 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 1844 5 %
Rwork0.1745 --
obs0.1762 36937 99.92 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.77 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4119 Å20 Å20 Å2
2---2.0262 Å20 Å2
3----6.3857 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 62 398 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063203
X-RAY DIFFRACTIONf_angle_d1.0424351
X-RAY DIFFRACTIONf_dihedral_angle_d13.5591176
X-RAY DIFFRACTIONf_chiral_restr0.072485
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.25691370.21042676X-RAY DIFFRACTION100
1.9514-2.00880.23461290.17472642X-RAY DIFFRACTION100
2.0088-2.07360.23491360.16732681X-RAY DIFFRACTION100
2.0736-2.14770.20961520.16242651X-RAY DIFFRACTION100
2.1477-2.23370.17551270.16132672X-RAY DIFFRACTION100
2.2337-2.33530.22251410.15932694X-RAY DIFFRACTION100
2.3353-2.45840.22461340.17372668X-RAY DIFFRACTION100
2.4584-2.61240.22891450.17462666X-RAY DIFFRACTION100
2.6124-2.8140.20341450.18362703X-RAY DIFFRACTION100
2.814-3.09710.22561540.18572694X-RAY DIFFRACTION100
3.0971-3.54490.20841350.18032723X-RAY DIFFRACTION100
3.5449-4.46470.18391410.15182774X-RAY DIFFRACTION100
4.4647-35.01530.20851680.18992849X-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)
10.6959-0.05540.28112.2264-0.11983.41550.0197-0.0369-0.02070.3183-0.0361-0.1047-0.1030.00760.02790.1259-0.0046-0.01390.1111-0.02040.1477-2.6347-1.446124.0332
21.51650.75670.38032.16460.03881.05920.04330.01420.012-0.1056-0.04790.09210.0035-0.0690.00550.11240.05230.00430.15180.0050.1205-14.0518-6.06916.3429
30.66810.0448-0.22511.3336-0.95871.74340.034-0.0448-0.0244-0.031-0.0493-0.09870.03730.13860.0150.08990.0294-0.01770.14-0.01370.1675-4.1633-17.221617.2123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -5:114)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 115:261)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 262:397)

+
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