[English] 日本語
Yorodumi
- PDB-5end: Crystal structure of beta-ketoacyl-acyl carrier protein reductase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5end
TitleCrystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG)(Q152A) from Vibrio cholerae
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / FabG / beta-ketoacyl-acyl carrier protein reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 FabG
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsHou, J. / Cooper, D.R. / Zheng, H. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Bacteriol. / Year: 2015
Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: Data collection
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_oper_list
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,1503
Polymers52,0582
Non-polymers921
Water88349
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,2996
Polymers104,1154
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area8840 Å2
ΔGint-58 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.995, 63.995, 190.474
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA5 - 865 - 86
21METMETILEILEBB5 - 865 - 86
12TRPTRPSERSERAA107 - 142107 - 142
22TRPTRPSERSERBB107 - 142107 - 142
13ASNASNPHEPHEAA154 - 187154 - 187
23ASNASNPHEPHEBB154 - 187154 - 187
14ARGARGASNASNAA212 - 242212 - 242
24ARGARGASNASNBB212 - 242212 - 242

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 26028.805 Da / Num. of mol.: 2 / Mutation: Q152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabG, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Tris, 20% PEG1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2015 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Number: 72363 / Rmerge(I) obs: 0.097 / Χ2: 0.86 / D res high: 2.55 Å / D res low: 50 Å / Num. obs: 14503 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.925010.0351.0984.6
5.496.9210.0490.7685
4.85.4910.050.8035
4.364.810.0541.1395
4.054.3610.0631.0855
3.814.0510.0740.9525
3.623.8110.0971.3695
3.463.6210.0860.8455
3.333.4610.1080.8435
3.213.3310.1510.7695
3.113.2110.1790.7365
3.023.1110.210.7575
2.943.0210.2540.7415
2.872.9410.2870.7345
2.812.8710.3810.7695
2.752.8110.3760.7655
2.692.7510.4790.7285.1
2.642.6910.6170.7865
2.592.6410.630.7895
2.552.5910.7550.7795
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.892
11K, H, -L20.108
ReflectionResolution: 2.55→50 Å / Num. obs: 14503 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Rrim(I) all: 0.108 / Χ2: 0.862 / Net I/av σ(I): 15.355 / Net I/σ(I): 6.4 / Num. measured all: 72363
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.5950.7556980.6590.3740.8440.779100
2.59-2.6450.637340.7480.3130.7050.789100
2.64-2.6950.6177340.7190.3070.6910.786100
2.69-2.755.10.4797020.8420.2340.5350.728100
2.75-2.8150.3767380.9020.1860.420.765100
2.81-2.8750.3817150.8830.1880.4260.769100
2.87-2.9450.2877280.9180.1410.3210.734100
2.94-3.0250.2547240.9390.1240.2840.741100
3.02-3.1150.217070.9580.1030.2350.757100
3.11-3.2150.1797420.970.0870.20.736100
3.21-3.3350.1517110.9640.0740.1680.769100
3.33-3.4650.1087320.9810.0520.120.843100
3.46-3.6250.0867280.9850.0420.0960.845100
3.62-3.8150.0977260.980.0470.1081.369100
3.81-4.0550.0747280.990.0360.0830.952100
4.05-4.3650.0637180.9890.0310.0711.08599.7
4.36-4.850.0547230.9890.0260.061.13999.7
4.8-5.4950.057310.9960.0230.0550.80399.7
5.49-6.9250.0497340.9960.0230.0550.768100
6.92-504.60.0357500.9930.0170.0391.09899.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
MOLREPphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.9 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 21.916 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.462 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 667 4.8 %RANDOM
Rwork0.2061 ---
obs0.2084 13264 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.77 Å2 / Biso mean: 44.008 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1--6.11 Å2-0 Å2-0 Å2
2---6.11 Å2-0 Å2
3---12.22 Å2
Refinement stepCycle: final / Resolution: 2.55→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 6 49 3266
Biso mean--43.91 30.82 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193244
X-RAY DIFFRACTIONr_bond_other_d0.0020.023150
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9634389
X-RAY DIFFRACTIONr_angle_other_deg1.06937184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85124.336113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20615516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2991521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02679
X-RAY DIFFRACTIONr_mcbond_it0.7642.1761810
X-RAY DIFFRACTIONr_mcbond_other0.7632.1761809
X-RAY DIFFRACTIONr_mcangle_it1.3533.2572252
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDNumberRms dev position (Å)
111353.89
25554.07
34622.36
44522.2
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 39 -
Rwork0.249 711 -
all-750 -
obs--72.46 %
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)
12.62050.4264-0.30883.9578-0.33872.84660.4662-0.32860.13670.5496-0.38760.2846-0.1076-0.1962-0.07860.1977-0.19420.09690.2581-0.10420.054110.5687-12.844720.2751
21.09020.8407-0.32222.90740.660820.2623-0.24450.010.4569-0.26370.0359-0.0466-0.03520.00140.203-0.1367-0.00150.2929-0.00360.050325.7852-7.85516.1707
32.962-1.27020.41654.5909-1.25241.4193-0.0207-0.11290.44430.5538-0.05450.3341-0.452-0.10380.07530.1901-0.03820.0350.2331-0.0880.16414.18641.70515.4935
44.39130.2696-0.08632.5992-0.73912.50260.1380.1719-0.23450.0777-0.08510.31060.2630.1662-0.05290.14370.0566-0.07550.2988-0.10390.13039.6417-15.787-16.6934
52.55370.42420.38351.21391.03211.60940.16810.67870.0878-0.2563-0.13040.0532-0.06410.2554-0.03770.14220.1451-0.03250.4491-0.01230.018318.1239-4.7735-20.6963
63.5739-0.99691.02133.241-1.13472.04350.22970.3049-0.1815-0.2745-0.277-0.17810.33760.35940.04720.15280.0395-0.00410.3122-0.05730.065322.8493-11.1698-6.3699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 102
2X-RAY DIFFRACTION2A103 - 181
3X-RAY DIFFRACTION3A182 - 246
4X-RAY DIFFRACTION4B2 - 54
5X-RAY DIFFRACTION5B55 - 164
6X-RAY DIFFRACTION6B165 - 246

+
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