[English] 日本語
Yorodumi
- PDB-4fw8: Crystal structure of FABG4 complexed with Coenzyme NADH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fw8
TitleCrystal structure of FABG4 complexed with Coenzyme NADH
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


long-chain fatty-acyl-CoA metabolic process / short-chain fatty acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / peptidoglycan-based cell wall / response to antibiotic / nucleotide binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-ZPG / 3-oxoacyl-(Acyl-carrier-protein) reductase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsDutta, D. / Bhattacharyya, S. / Das, A.K.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structure of hexanoyl-CoA bound to beta-ketoacyl reductase FabG4 of Mycobacterium tuberculosis
Authors: Dutta, D. / Bhattacharyya, S. / Roychowdhury, A. / Biswas, R. / Das, A.K.
History
DepositionJun 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-oxoacyl-(Acyl-carrier-protein) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,5989
Polymers187,5124
Non-polymers3,0865
Water3,891216
1
A: 3-oxoacyl-(Acyl-carrier-protein) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5115
Polymers93,7562
Non-polymers1,7553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-46 kcal/mol
Surface area29870 Å2
MethodPISA
2
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0874
Polymers93,7562
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-36 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.333, 71.304, 93.293
Angle α, β, γ (deg.)104.990, 97.080, 93.660
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
3-oxoacyl-(Acyl-carrier-protein) reductase / Ketoreductase / PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 (3-KETOACYL-ACYL CARRIER ...Ketoreductase / PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 (3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE)


Mass: 46878.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: O53665, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-ZPG / (2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES PH 6.5, 47% (v/v) POLYPROPYLENE GLYCOL P400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.786→89.166 Å / Num. all: 37439 / Num. obs: 37439 / % possible obs: 96.2 % / Redundancy: 3.9 % / Rsym value: 0.113 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.79-2.943.80.5840.5031.51919450510.2950.5840.503389.1
2.94-3.1240.3920.342.32080152220.1970.3920.344.496.4
3.12-3.3340.2810.2433.21946248950.1410.2810.2435.897
3.33-3.640.1710.1485.21820245750.0860.1710.1489.197.3
3.6-3.9440.1270.10971691242560.0630.1270.10911.897.8
3.94-4.4140.090.0789.81514738130.0450.090.07815.698
4.41-5.0940.0750.06511.71346933950.0380.0750.06518.398.5
5.09-6.2340.0830.07210.51142128910.0420.0830.07216.598.9
6.23-8.813.90.0590.05113.7872922250.030.0590.05122.299.3
8.81-19.8583.90.0380.03219.3432011160.0190.0380.03231.990.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→19.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8409 / SU B: 34.677 / SU ML: 0.305 / SU R Cruickshank DPI: 0.3052 / SU Rfree: 0.4043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1889 5 %RANDOM
Rwork0.1618 ---
obs0.1656 37439 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 40.963 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0.97 Å2-2.66 Å2
2--1.21 Å20.33 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.79→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12057 0 189 216 12462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212435
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.99216938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43651665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84823.878459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.446151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561591
X-RAY DIFFRACTIONr_chiral_restr0.0940.22023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219323
X-RAY DIFFRACTIONr_mcbond_it0.5221.58251
X-RAY DIFFRACTIONr_mcangle_it1213066
X-RAY DIFFRACTIONr_scbond_it1.58334184
X-RAY DIFFRACTIONr_scangle_it2.7454.53872
LS refinement shellResolution: 2.786→2.859 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 117 -
Rwork0.283 2248 -
all-2365 -
obs--82.06 %
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)
10.57020.05180.03610.53910.05841.05840.014-0.119-0.00250.02370.0245-0.01010.0653-0.204-0.03850.0304-0.01250.01660.09050.02670.07631.6399-0.16821.0727
20.57610.0115-0.24630.61660.12151.098-0.00710.04680.0747-0.01020.0258-0.047-0.18360.2513-0.01870.0631-0.05440.00760.08770.01590.066625.278216.4538-12.7687
31.2952-0.09370.6861.00590.09550.94770.0050.08080.07240.05190.0521-0.1256-0.0020.0274-0.05710.02730.02670.01350.05710.00140.0522-16.0348-25.532830.4816
41.23350.04980.59790.87210.21480.73840.133-0.0497-0.19430.2530.0269-0.06850.3163-0.1074-0.15990.2684-0.0102-0.10210.03330.0040.0584-20.9897-55.310342.217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 454
2X-RAY DIFFRACTION2B20 - 454
3X-RAY DIFFRACTION3C29 - 454
4X-RAY DIFFRACTION4D29 - 454

+
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