[English] 日本語
Yorodumi
- PDB-6nrp: Putative short-chain dehydrogenase/reductase (SDR) from Acinetoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nrp
TitlePutative short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii
Components3-oxoacyl-ACP reductase FabG
KeywordsOXIDOREDUCTASE / Short-chain dehydrogenase/reductase / SDR / Rossmann fold / apo
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase, putative / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCross, E.M. / Smith, K.M. / Shaw, K.I. / Aragao, D. / Forwood, J.K.
CitationJournal: Sci Rep / Year: 2021
Title: Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases.
Authors: Cross, E.M. / Adams, F.G. / Waters, J.K. / Aragao, D. / Eijkelkamp, B.A. / Forwood, J.K.
History
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 29, 2023Group: Database references / Category: citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase FabG
B: 3-oxoacyl-ACP reductase FabG
C: 3-oxoacyl-ACP reductase FabG
D: 3-oxoacyl-ACP reductase FabG


Theoretical massNumber of molelcules
Total (without water)114,8754
Polymers114,8754
Non-polymers00
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-72 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.479, 89.479, 239.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

-
Components

#1: Protein
3-oxoacyl-ACP reductase FabG / 3-oxoacyl-ACPreductase / Beta-ketoacyl-ACP reductase


Mass: 28718.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabG_5, fabG_1, fabG_18, fabG_23, fabG_3, fabG_4, Aba10042_16075, B9X91_04165, CEJ63_07105, SAMEA104305229_00942, SAMEA104305242_02267, SAMEA104305268_00730, SAMEA104305271_00024, ...Gene: fabG_5, fabG_1, fabG_18, fabG_23, fabG_3, fabG_4, Aba10042_16075, B9X91_04165, CEJ63_07105, SAMEA104305229_00942, SAMEA104305242_02267, SAMEA104305268_00730, SAMEA104305271_00024, SAMEA104305315_07776, SAMEA104305320_01205, SAMEA104305325_01875, SAMEA104305337_07930
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1K1L6W4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: Cubic
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M magnesium acetate, 0.1M sodium acetate pH 4.5, 8% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→24.99 Å / Num. obs: 88460 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 15.161 Å2 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.05 / Rrim(I) all: 0.148 / Χ2: 0.94 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→1.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4426 / Rpim(I) all: 0.236 / Rrim(I) all: 0.652 / Χ2: 0.92 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IIU

4iiu


Resolution: 1.9→24.987 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3
RfactorNum. reflection% reflection
Rfree0.1917 4504 5.1 %
Rwork0.1702 --
obs0.1713 88293 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 0 484 7616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077220
X-RAY DIFFRACTIONf_angle_d0.8439755
X-RAY DIFFRACTIONf_dihedral_angle_d22.3682661
X-RAY DIFFRACTIONf_chiral_restr0.0611157
X-RAY DIFFRACTIONf_plane_restr0.0051262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.26431710.21542698X-RAY DIFFRACTION99
1.9216-1.94420.25541400.21162791X-RAY DIFFRACTION100
1.9442-1.96790.2231520.19462702X-RAY DIFFRACTION100
1.9679-1.99280.19551350.1762807X-RAY DIFFRACTION100
1.9928-2.0190.18731330.1742744X-RAY DIFFRACTION100
2.019-2.04670.20881830.17492729X-RAY DIFFRACTION100
2.0467-2.07590.22751530.18112766X-RAY DIFFRACTION100
2.0759-2.10690.21491450.17842725X-RAY DIFFRACTION100
2.1069-2.13980.19561470.17412789X-RAY DIFFRACTION100
2.1398-2.17490.22631420.17272777X-RAY DIFFRACTION100
2.1749-2.21230.20251770.16992750X-RAY DIFFRACTION100
2.2123-2.25250.25451390.17462762X-RAY DIFFRACTION100
2.2525-2.29580.21261470.16872803X-RAY DIFFRACTION100
2.2958-2.34270.19151620.16612740X-RAY DIFFRACTION100
2.3427-2.39360.20821710.17052751X-RAY DIFFRACTION100
2.3936-2.44920.22441280.16292794X-RAY DIFFRACTION100
2.4492-2.51040.18861470.17282800X-RAY DIFFRACTION100
2.5104-2.57820.21921390.17782796X-RAY DIFFRACTION100
2.5782-2.6540.2121410.17362763X-RAY DIFFRACTION100
2.654-2.73950.21011500.17092798X-RAY DIFFRACTION100
2.7395-2.83730.1951630.17572763X-RAY DIFFRACTION100
2.8373-2.95080.17721330.17612814X-RAY DIFFRACTION100
2.9508-3.08480.17941350.17442850X-RAY DIFFRACTION100
3.0848-3.24710.20561320.18042811X-RAY DIFFRACTION100
3.2471-3.45010.20821390.17232825X-RAY DIFFRACTION100
3.4501-3.71570.1731230.16352861X-RAY DIFFRACTION100
3.7157-4.08810.17311770.15762830X-RAY DIFFRACTION100
4.0881-4.67630.13491620.14412852X-RAY DIFFRACTION100
4.6763-5.8790.17691700.16662870X-RAY DIFFRACTION100
5.879-24.98910.1671680.16933028X-RAY DIFFRACTION100

+
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