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- PDB-5vp5: Crystal structure of a 3-oxoacyl-acyl-carrier protein reductase F... -

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Basic information

Entry
Database: PDB / ID: 5vp5
TitleCrystal structure of a 3-oxoacyl-acyl-carrier protein reductase FabG4 from Mycobacterium smegmatis bound to NAD
Components3-oxoacyl-acyl-carrier protein reductase FabG4
KeywordsOXIDOREDUCTASE / NIAID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis.
Authors: Ran, X. / Parikh, P. / Abendroth, J. / Arakaki, T.L. / Clifton, M.C. / Edwards, T.E. / Lorimer, D.D. / Mayclin, S. / Staker, B.L. / Myler, P. / McLaughlin, K.J.
History
DepositionMay 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-acyl-carrier protein reductase FabG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6684
Polymers48,9331
Non-polymers7343
Water8,107450
1
A: 3-oxoacyl-acyl-carrier protein reductase FabG4
hetero molecules

A: 3-oxoacyl-acyl-carrier protein reductase FabG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3358
Polymers97,8672
Non-polymers1,4696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8270 Å2
ΔGint-73 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.580, 60.610, 76.270
Angle α, β, γ (deg.)90.000, 126.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1045-

HOH

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Components

#1: Protein 3-oxoacyl-acyl-carrier protein reductase FabG4 / Oxidoreductase / short chain dehydrogenase/reductase family protein


Mass: 48933.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: fabG4, MSMEG_0372, MSMEI_0365 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QPE7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MysmA.00010.a.A1.PW28467 at 19.87 mg/mL with 4 mM NAD against MCSG1 screen condition E3 50 mM MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 550 MME soaked overnight with 10 mM NAD, crystal tracking ID ...Details: MysmA.00010.a.A1.PW28467 at 19.87 mg/mL with 4 mM NAD against MCSG1 screen condition E3 50 mM MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 550 MME soaked overnight with 10 mM NAD, crystal tracking ID 271652e3, unique puck ID hnk3-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.625 Å / Num. obs: 34407 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.336 % / Biso Wilson estimate: 14.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.042 / Χ2: 1.008 / Net I/σ(I): 22.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.9550.1277.4225130.9750.15598.4
1.85-1.93.440.10110.4724710.9860.1299.8
1.9-1.953.4760.08912.1224090.990.10599.7
1.95-2.013.420.07613.8323300.9920.0999.5
2.01-2.083.2960.06715.6122720.9930.08199.5
2.08-2.153.220.05717.8121740.9950.06899.5
2.15-2.233.4870.05419.4521220.9960.06499.3
2.23-2.323.460.04721.7120320.9970.05699.4
2.32-2.433.3930.04522.7819640.9970.05499.4
2.43-2.553.2060.04224.0218660.9970.05199.1
2.55-2.683.3520.03826.917810.9970.04598.9
2.68-2.853.4550.03429.4116740.9980.04199.3
2.85-3.043.4170.03132.3215860.9980.03798.9
3.04-3.293.2020.02933.7414760.9980.03598.7
3.29-3.63.320.02539.1513660.9990.0399.2
3.6-4.023.4490.02341.1512260.9990.02798.5
4.02-4.653.3030.02242.510930.9990.02698.9
4.65-5.693.2360.02341.019200.9990.02898.3
5.69-8.053.3720.02542.47170.9980.0397.6
8.05-48.6253.1130.02546.014150.9990.0396.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(dev_2744)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0B

3u0b


Resolution: 1.8→48.625 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 15.82
RfactorNum. reflection% reflection
Rfree0.177 2086 6.06 %
Rwork0.1355 --
obs0.1379 34404 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.58 Å2 / Biso mean: 18.2766 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 1.8→48.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 46 451 3451
Biso mean--17.56 29.23 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063111
X-RAY DIFFRACTIONf_angle_d0.7914266
X-RAY DIFFRACTIONf_chiral_restr0.057513
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d10.7751888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.84180.20681570.16192105226298
1.8418-1.88790.23011520.153521202272100
1.8879-1.93890.20351450.144521272272100
1.9389-1.9960.18661170.144621762293100
1.996-2.06040.20091360.14121522288100
2.0604-2.13410.20361300.143221792309100
2.1341-2.21950.18861310.140121512282100
2.2195-2.32050.16061300.13521562286100
2.3205-2.44280.20271750.136821202295100
2.4428-2.59590.1721490.136721312280100
2.5959-2.79630.15431390.134221622301100
2.7963-3.07770.17851660.131821242290100
3.0777-3.52290.1541220.128321852307100
3.5229-4.4380.15411080.11552210231899
4.438-48.64240.16691290.14312220234999
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)
12.4072-0.72260.0862.4764-0.97660.95730.03720.14750.0173-0.1674-0.0759-0.12310.00550.05720.04450.1407-0.01880.02470.142-0.02320.076819.027110.1608-22.4505
20.65810.00660.26430.7928-0.18471.42960.0045-0.00920.00080.01220.0025-0.0296-0.03810.1113-0.00560.0684-0.00640.01650.0931-0.00680.073214.18765.6075-10.8026
35.6914-1.75250.21432.11220.00021.2362-0.01380.22590.1235-0.05150.0183-0.0719-0.08840.0374-0.02750.1039-0.0271-0.00350.08160.0140.046-8.03118.205-28.215
41.58751.4423-2.53132.8988-3.30334.9893-0.0230.15070.29710.00680.24750.2-0.1233-0.3244-0.24430.0848-0.0001-0.03070.14060.01860.1148-21.046310.3885-28.5682
50.6069-0.0427-0.11061.30261.67193.58980.0223-0.05280.0565-0.0465-0.0330.0749-0.1757-0.25140.07970.08570.0149-0.01250.08280.02150.1028-20.65187.3353-16.0718
60.70720.36930.22381.36011.47013.0296-0.0026-0.03720.00710.04020.0617-0.036-0.01220.0373-0.06950.08050.0153-0.00980.07910.01860.0945-12.89273.1079-13.6758
71.98060.0165-0.23330.14340.12112.1190.03560.05030.23260.0052-0.0382-0.0871-0.24930.033-0.05580.11270.0028-0.01240.09740.01160.1172-6.7538.9136-11.2618
82.4590.24270.27523.3102-0.15031.6766-0.0148-0.18150.14260.2188-0.02940.0061-0.13840.0880.01750.0772-0.02470.00040.1036-0.01230.0708-0.1017.9097-15.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 78 )A26 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 202 )A79 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 241 )A203 - 241
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 268 )A242 - 268
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 316 )A269 - 316
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 353 )A317 - 353
7X-RAY DIFFRACTION7chain 'A' and (resid 354 through 416 )A354 - 416
8X-RAY DIFFRACTION8chain 'A' and (resid 417 through 450 )A417 - 450

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