[English] 日本語
Yorodumi
- PDB-6ci8: Structure of the microcompartment-associated aminoacetone dehydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ci8
TitleStructure of the microcompartment-associated aminoacetone dehydrogenase
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / dehydrogenase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
Similarity search - Function
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-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMallette, E. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Biochemistry / Year: 2018
Title: Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.
Authors: Mallette, E. / Kimber, M.S.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2524
Polymers54,1812
Non-polymers712
Water10,881604
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5038
Polymers108,3614
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area18260 Å2
ΔGint-182 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.240, 104.240, 80.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

21B-635-

HOH

31B-638-

HOH

41B-652-

HOH

51B-697-

HOH

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 27090.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0269 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0QP46, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: tri-sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→45.137 Å / Num. obs: 56008 / % possible obs: 100 % / Redundancy: 6.208 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.06 / Χ2: 0.977 / Net I/σ(I): 19.86 / Num. measured all: 347712 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.746.2060.683.0440710.8650.741100
1.74-1.796.2070.5133.8940110.9070.558100
1.79-1.846.210.4034.9438960.9460.439100
1.84-1.96.2160.296.6638020.9690.316100
1.9-1.966.2370.2258.4536700.9810.246100
1.96-2.036.2510.16910.7735420.9880.185100
2.03-2.116.2260.1313.6834100.9920.142100
2.11-2.196.2530.10516.4133220.9950.115100
2.19-2.296.2430.0918.5631530.9960.09999.9
2.29-2.46.2380.07521.5930580.9960.083100
2.4-2.536.270.06424.5429040.9970.07100
2.53-2.696.2530.05528.0327320.9970.06199.9
2.69-2.876.2650.04631.7925770.9980.051100
2.87-3.16.2310.04335.5824070.9980.04799.9
3.1-3.46.2120.03640.8822130.9980.03999.9
3.4-3.86.1520.03244.720120.9980.03699.9
3.8-4.396.1380.03147.4818010.9980.03499.9
4.39-5.386.0970.03148.0715240.9990.03499.9
5.38-7.65.9420.0347.0712020.9980.03499.9
7.6-45.1375.5380.03148.217010.9990.03599.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIH

3rih


Resolution: 1.7→45.137 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.1698 2801 5 %
Rwork0.1442 --
obs0.1454 56008 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.49 Å2 / Biso mean: 23.5985 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: final / Resolution: 1.7→45.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 2 604 4388
Biso mean--24.57 32.64 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173914
X-RAY DIFFRACTIONf_angle_d1.3335341
X-RAY DIFFRACTIONf_chiral_restr0.1639
X-RAY DIFFRACTIONf_plane_restr0.008709
X-RAY DIFFRACTIONf_dihedral_angle_d8.4923121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.72930.25541370.213226042741
1.7293-1.76080.24711400.198626492789
1.7608-1.79460.20471390.180426462785
1.7946-1.83130.20591390.172526492788
1.8313-1.87110.17651370.15726072744
1.8711-1.91460.19151400.150826512791
1.9146-1.96250.18161390.150726442783
1.9625-2.01560.1771390.143726392778
2.0156-2.07490.18521380.145326222760
2.0749-2.14180.16831390.13826412780
2.1418-2.21840.17371400.132526572797
2.2184-2.30720.16271400.135826592799
2.3072-2.41220.16811390.13226382777
2.4122-2.53940.1611410.140726842825
2.5394-2.69840.16621390.141726512790
2.6984-2.90680.18281410.143726722813
2.9068-3.19920.16491410.14426792820
3.1992-3.6620.14061420.135826942836
3.662-4.6130.13491420.123627002842
4.613-45.15310.17791490.149728232972
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)
12.4225-0.0345-0.65371.5683-0.57621.6086-0.0515-0.2924-0.14680.05730.10120.2910.0194-0.3599-0.0010.0558-0.01460.01860.24840.02330.192210.779876.007743.4233
22.84591.20260.49812.72381.32574.2692-0.09650.1186-0.3731-0.06290.10.3810.2691-0.45430.00360.0882-0.0492-0.00780.2963-0.00570.31263.250473.809333.4246
33.28140.0983-2.56681.4087-0.28433.28090.0783-0.0395-0.0565-0.04640.04680.39040.0183-0.3978-0.05150.0482-0.0396-0.00970.2830.01590.26465.677477.347933.7491
40.9081-0.3770.21160.9958-0.18830.52410.03010.1014-0.0696-0.0959-0.01580.16090.1001-0.12040.0020.0785-0.0318-0.00980.1453-0.01450.112421.193773.211329.7877
52.36390.4682-0.67712.9647-0.66721.9337-0.09960.1314-0.3989-0.38940.10860.47280.3735-0.41280.13220.1251-0.0814-0.05440.1977-0.00540.240816.384864.294438.4106
61.95420.71970.24173.58460.07122.37780.03230.1442-0.8779-0.3566-0.0440.39870.7169-0.52580.00710.308-0.17820.00310.2672-0.00230.477315.424950.380643.3957
72.46540.97370.29921.6647-0.06430.8475-0.0184-0.22520.03790.0828-0.00690.11970.0425-0.23740.00840.084-0.00490.01460.163-0.01010.10421.138675.191446.9303
82.3418-0.34760.31068.4550.04291.9183-0.0701-0.0937-0.58230.00440.11610.08630.4591-0.2066-0.06180.1915-0.07670.03110.1420.00990.192327.810553.68244.9468
92.324-1.02640.51231.5160.47562.02730.21480.66310.1692-0.4013-0.2651-0.22420.11530.3520.02610.30640.1020.0640.3401-0.0050.123551.133761.488112.5117
104.9511-1.1372-1.49910.88660.91321.48410.09110.37230.089-0.4009-0.1556-0.1790.11560.2059-0.01810.37140.13820.0810.50030.00790.116847.350462.49017.1577
111.1526-0.6281-0.01861.4074-0.09280.43290.16020.4895-0.0105-0.3396-0.17480.04220.18150.04330.04780.26320.0431-0.02120.2582-0.05830.075335.733463.704714.5832
121.2835-0.40110.33881.52840.65491.41740.08530.2416-0.0233-0.1388-0.0715-0.07310.15090.03630.02120.11810.00850.00790.1083-0.01020.063740.285465.200825.591
131.78060.50.03662.3571-0.06141.56260.03030.10920.2421-0.1181-0.084-0.0898-0.07770.0950.02970.08550.02740.00280.08490.02950.119450.671168.67232.5336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 50 )A30 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 67 )A51 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 178 )A68 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 199 )A179 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 217 )A200 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 238 )A218 - 238
8X-RAY DIFFRACTION8chain 'A' and (resid 239 through 258 )A239 - 258
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 50 )B1 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 67 )B51 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 133 )B68 - 133
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 199 )B134 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 258 )B200 - 258

+
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