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- PDB-8aew: Malonyl-CoA reductase from Chloroflexus aurantiacus - N-terminal Apo -

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Basic information

Entry
Database: PDB / ID: 8aew
TitleMalonyl-CoA reductase from Chloroflexus aurantiacus - N-terminal Apo
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Rossmann fold / bi-functional enzyme / reductase / malonyl-CoA / 3-hydroxypropionate / 3-HP cycle
Function / homologyfatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsKabasakal, B.V. / Murray, J.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/F017324/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
Citation
Journal: Biochimie / Year: 2023
Title: Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction.
Authors: Kabasakal, B.V. / Cotton, C.A.R. / Murray, J.W.
#1: Journal: Biorxiv / Year: 2023
Title: Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA Reductase controls the reaction
Authors: Kabasakal, B.V. / Cotton, C.A.R. / Murray, J.W.
History
DepositionJul 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Short-chain dehydrogenase/reductase SDR
A: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)117,6612
Polymers117,6612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-18 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.761, 86.787, 260.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 58830.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria)
Gene: Caur_2614 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WIU3
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate, pH 6.5, 40% (w/v) MPD 5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.72→82.34 Å / Num. obs: 68074 / % possible obs: 98.5 % / Redundancy: 2 % / Biso Wilson estimate: 58.25 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1095 / Rpim(I) all: 0.1095 / Rrim(I) all: 0.1548 / Net I/σ(I): 7.5
Reflection shellResolution: 2.72→2.817 Å / Redundancy: 2 % / Rmerge(I) obs: 1.273 / Num. unique obs: 6553 / CC1/2: 0.478 / CC star: 0.804 / Rpim(I) all: 1 / Rrim(I) all: 1 / % possible all: 96.09

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→82.34 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2904 1708 5.05 %
Rwork0.2437 --
obs0.2462 33849 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→82.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8019 0 0 0 8019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088157
X-RAY DIFFRACTIONf_angle_d1.12211099
X-RAY DIFFRACTIONf_dihedral_angle_d6.5311165
X-RAY DIFFRACTIONf_chiral_restr0.0621291
X-RAY DIFFRACTIONf_plane_restr0.0171477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.80.45261470.40432532X-RAY DIFFRACTION96
2.8-2.890.43421320.39322594X-RAY DIFFRACTION96
2.89-2.990.40351410.38262623X-RAY DIFFRACTION99
2.99-3.110.44651390.36742604X-RAY DIFFRACTION97
3.11-3.260.44071490.3292642X-RAY DIFFRACTION99
3.26-3.430.37171380.31522660X-RAY DIFFRACTION98
3.43-3.640.32341220.27452699X-RAY DIFFRACTION99
3.64-3.920.27341370.24422693X-RAY DIFFRACTION99
3.92-4.320.26271470.20562674X-RAY DIFFRACTION99
4.32-4.940.21281340.18142750X-RAY DIFFRACTION100
4.94-6.230.261660.21662749X-RAY DIFFRACTION99
6.23-100.2231560.17172921X-RAY DIFFRACTION100
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)
12.2801-0.5980.74282.11533.61967.9525-0.39270.07230.3351-0.7976-0.21010.2862-1.7402-0.13690.5130.6906-0.0588-0.17240.47050.02830.6017-1.881127.4944-27.5487
26.31050.6649-2.20782.0642-2.98466.7413-0.30510.64150.90450.06830.33510.9431-1.1955-1.9353-0.07891.14980.1114-0.16771.34560.02470.8471-25.953322.8145-36.9983
30.8563-0.2346-1.41460.4438-0.06844.0273-0.23370.2273-0.0628-0.2788-0.06560.12050.0313-0.16230.2980.6892-0.0639-0.00440.5852-0.0690.6141-8.214410.1902-40.6047
43.94090.2514-0.27262.3488-0.15036.13141.17-0.2658-0.5937-1.9270.2003-1.0212-0.82121.5490.02391.092-0.31250.14511.28920.08820.909812.866413.0049-67.4886
52.01460.6350.52693.96691.80598.7909-0.34290.29360.0764-0.6105-0.07110.1771-0.72480.1160.33050.49240.0035-0.03110.5708-0.04340.5114-3.675612.8683-53.1221
62.196-0.7674-0.76062.64422.36284.6731-0.3322-0.1395-0.26950.9206-0.07610.13851.97010.19760.35731.07370.09180.21230.48840.02770.5583-12.7488-5.2409-8.2341
75.61981.3662.57472.7262-1.43283.0325-0.4838-1.115-0.880.29840.6432-1.11411.29890.591-0.06191.5190.23890.00490.7697-0.05540.878110.6303-11.4544-16.3168
87.96570.1491-1.27551.9567-0.24814.2674-0.0403-0.3675-0.16290.224-0.18830.0330.62730.42770.26790.61520.0070.02530.4227-0.02230.47931.2828.12-13.6985
90.92921.65911.55783.68351.24145.149-0.25260.3409-0.0634-0.4310.18850.23921.54960.20670.04241.1120.07670.14650.6072-0.0950.6783-12.0528-18.7746-39.7263
100.61980.65950.6175.86243.00843.8570.03730.2873-0.22631.5395-0.7241.19323.1216-1.01420.8012.0398-0.30510.4070.8398-0.23070.9292-21.648-27.3925-31.3813
112.8451-0.56030.44466.80142.55714.2138-1.12470.3562-0.8511.86090.5014-0.01042.45740.3855-0.45651.8860.29860.2060.6038-0.11240.6572-7.3765-24.2699-33.3919
121.57890.32880.39735.63081.75115.1322-0.01970.2704-0.22890.07570.0648-0.40731.42350.62650.04630.99750.1490.09980.5739-0.05310.5506-7.1281-16.3406-37.4738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 206 )
2X-RAY DIFFRACTION2chain 'B' and (resid 207 through 233 )
3X-RAY DIFFRACTION3chain 'B' and (resid 234 through 339 )
4X-RAY DIFFRACTION4chain 'B' and (resid 340 through 370 )
5X-RAY DIFFRACTION5chain 'B' and (resid 371 through 548 )
6X-RAY DIFFRACTION6chain 'A' and (resid 4 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 233 )
8X-RAY DIFFRACTION8chain 'A' and (resid 234 through 274 )
9X-RAY DIFFRACTION9chain 'A' and (resid 275 through 339 )
10X-RAY DIFFRACTION10chain 'A' and (resid 340 through 424 )
11X-RAY DIFFRACTION11chain 'A' and (resid 425 through 466 )
12X-RAY DIFFRACTION12chain 'A' and (resid 467 through 548 )

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