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- PDB-8aeo: Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 8aeo
TitleMalonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal R773A variant
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Rossmann fold / site-directed mutagenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.76 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 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6205
Polymers73,2351
Non-polymers3844
Water7,963442
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,23910
Polymers146,4712
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5710 Å2
ΔGint-135 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.715, 140.264, 73.838
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1581-

HOH

21A-1814-

HOH

31A-1819-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 73235.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: ATCC 29366 / DSM 635 / J-10-fl / Gene: Caur_2614 / Production host: Escherichia coli (E. coli) / References: UniProt: A9WIU3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Sodium citrate tribasic dihydrate, 1 M Ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.76→48.77 Å / Num. obs: 161792 / % possible obs: 98.34 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.82 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03436 / Rpim(I) all: 0.03436 / Rrim(I) all: 0.0486 / Net I/σ(I): 10.56
Reflection shellResolution: 1.763→1.826 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 16583 / CC1/2: 0.592 / CC star: 0.862 / Rpim(I) all: 0.354 / Rrim(I) all: 0.5007 / % possible all: 99.44

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A30

8a30


Resolution: 1.76→48.77 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 7852 4.9 %
Rwork0.1721 --
obs0.1736 160185 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 20 442 5324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064968
X-RAY DIFFRACTIONf_angle_d0.7466743
X-RAY DIFFRACTIONf_dihedral_angle_d16.5451842
X-RAY DIFFRACTIONf_chiral_restr0.048770
X-RAY DIFFRACTIONf_plane_restr0.007884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.36362460.33085097X-RAY DIFFRACTION94
1.78-1.80.33923030.30265303X-RAY DIFFRACTION97
1.8-1.830.30612620.29385268X-RAY DIFFRACTION97
1.83-1.850.29522550.2715292X-RAY DIFFRACTION97
1.85-1.870.34783020.27475250X-RAY DIFFRACTION97
1.87-1.90.34982890.28955260X-RAY DIFFRACTION97
1.9-1.930.30862550.29065277X-RAY DIFFRACTION96
1.93-1.950.33773000.28225100X-RAY DIFFRACTION95
1.95-1.990.29022400.25575240X-RAY DIFFRACTION96
1.99-2.020.23822540.22635308X-RAY DIFFRACTION96
2.02-2.050.25972860.20635185X-RAY DIFFRACTION96
2.05-2.090.21642500.20065237X-RAY DIFFRACTION95
2.09-2.130.21492910.19055155X-RAY DIFFRACTION96
2.13-2.170.20842640.18645225X-RAY DIFFRACTION96
2.17-2.220.24522550.20555146X-RAY DIFFRACTION95
2.22-2.270.27332980.23454994X-RAY DIFFRACTION93
2.27-2.330.21672530.20745035X-RAY DIFFRACTION93
2.33-2.390.26812630.19035030X-RAY DIFFRACTION92
2.39-2.460.19882560.17485016X-RAY DIFFRACTION92
2.46-2.540.25282410.17675012X-RAY DIFFRACTION92
2.54-2.630.25722410.17394987X-RAY DIFFRACTION91
2.63-2.740.18252270.17895073X-RAY DIFFRACTION91
2.74-2.860.24132560.18464917X-RAY DIFFRACTION90
2.86-3.010.20722500.18184766X-RAY DIFFRACTION89
3.01-3.20.19082620.17634819X-RAY DIFFRACTION88
3.2-3.450.19842270.16034751X-RAY DIFFRACTION87
3.45-3.80.17922610.14474850X-RAY DIFFRACTION89
3.8-4.350.14632590.12854820X-RAY DIFFRACTION89
4.35-5.470.13522440.1264895X-RAY DIFFRACTION90
5.48-100.16882620.14685025X-RAY DIFFRACTION93
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)
10.8218-0.44640.08112.46310.74441.0743-0.0043-0.0114-0.16630.1056-0.04810.15350.0789-0.03670.0520.19790.00820.02340.280.03740.2427-5.769712.720116.8654
24.3738-0.53421.0143.82091.05613.5565-0.1934-0.30690.00880.40970.21850.3507-0.0167-0.05-0.00280.24070.07320.02410.2696-0.00930.3285-36.162844.000114.8103
35.303-4.7831-0.46864.55760.65620.16630.36430.6471-0.2011-0.3989-0.55340.5712-0.1854-0.18160.1850.30730.0644-0.02420.4026-0.0320.4382-19.219117.22880.6208
40.1308-0.3091-0.32381.96321.12930.96840.07790.13410.0599-0.4992-0.0869-0.0409-0.494-0.06380.01770.50480.0051-0.01160.41380.05170.3134-2.766943.58029.7201
50.7681-0.3818-0.4332.42610.81191.6435-0.0362-0.00010.12930.06340.0053-0.2107-0.34870.12150.03820.3444-0.028-0.04580.31480.02780.2305-2.426644.769824.8161
60.6704-0.4180.79294.1736-1.13642.99890.05770.28770.2775-0.457-0.1844-0.3156-0.2440.06170.11570.38570.00360.04870.36660.04650.2405-2.75945.46699.5686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 562 through 784 )
2X-RAY DIFFRACTION2chain 'A' and (resid 785 through 898 )
3X-RAY DIFFRACTION3chain 'A' and (resid 899 through 937 )
4X-RAY DIFFRACTION4chain 'A' and (resid 938 through 1000 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1001 through 1127 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1128 through 1208 )

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