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- PDB-8a8t: Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 8a8t
TitleMalonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal NADP and malonate bound
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Malonyl-CoA / Chloroflexus aurantiacus / reductase / 3-hydroxypropionate / 3-HP cycle / bi-functional enzyme / carbon fixation
Function / homology
Function and homology information


fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding
Similarity search - Function
short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
MALONATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
DepositionJun 24, 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)74,1673
Polymers73,3211
Non-polymers8452
Water5,080282
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3346
Polymers146,6432
Non-polymers1,6914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7470 Å2
ΔGint-16 kcal/mol
Surface area47780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.960, 126.290, 74.330
Angle α, β, γ (deg.)90.00, 104.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1535-

HOH

21A-1666-

HOH

31A-1677-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 73321.453 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8 M succinic acid, pH 7.0, 0.5 mM NADPH co-crystallised

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.11→63.15 Å / Num. obs: 100168 / % possible obs: 98.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 42.78 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03785 / Rpim(I) all: 0.03785 / Rrim(I) all: 0.05353 / Net I/σ(I): 11.14
Reflection shellResolution: 2.11→2.185 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5348 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 5221 / CC1/2: 0.624 / CC star: 0.877 / Rpim(I) all: 0.5348 / Rrim(I) all: 0.7564 / % possible all: 99.87

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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: 2.11→63.15 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 4964 4.96 %
Rwork0.1815 --
obs0.1833 100168 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→63.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 55 282 5235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075092
X-RAY DIFFRACTIONf_angle_d0.896926
X-RAY DIFFRACTIONf_dihedral_angle_d15.5961900
X-RAY DIFFRACTIONf_chiral_restr0.049789
X-RAY DIFFRACTIONf_plane_restr0.008910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.130.35611250.32143292X-RAY DIFFRACTION100
2.13-2.160.36561880.3043219X-RAY DIFFRACTION100
2.16-2.190.3191480.30353378X-RAY DIFFRACTION100
2.19-2.210.31881540.30513071X-RAY DIFFRACTION100
2.21-2.240.35151740.35153304X-RAY DIFFRACTION99
2.24-2.270.45621670.40753142X-RAY DIFFRACTION98
2.27-2.310.32441870.29513238X-RAY DIFFRACTION100
2.31-2.340.31041780.24933166X-RAY DIFFRACTION100
2.34-2.380.29771880.24583233X-RAY DIFFRACTION100
2.38-2.420.23251740.22563230X-RAY DIFFRACTION100
2.42-2.460.23791770.22653227X-RAY DIFFRACTION100
2.46-2.50.2741590.22053194X-RAY DIFFRACTION100
2.5-2.550.27442150.21673154X-RAY DIFFRACTION100
2.55-2.60.27961770.21193267X-RAY DIFFRACTION100
2.6-2.660.21161640.20733220X-RAY DIFFRACTION100
2.66-2.720.20991500.20393240X-RAY DIFFRACTION100
2.72-2.790.25271840.19853233X-RAY DIFFRACTION100
2.79-2.860.23011800.19813246X-RAY DIFFRACTION100
2.86-2.950.24261460.20653162X-RAY DIFFRACTION99
2.95-3.040.25051460.20443254X-RAY DIFFRACTION99
3.04-3.150.29121770.21543182X-RAY DIFFRACTION98
3.15-3.280.24661450.213081X-RAY DIFFRACTION96
3.28-3.430.22591510.17973123X-RAY DIFFRACTION96
3.43-3.610.21851450.16453085X-RAY DIFFRACTION94
3.61-3.830.19031590.15753026X-RAY DIFFRACTION93
3.83-4.130.16811540.153000X-RAY DIFFRACTION94
4.13-4.540.15421700.13033025X-RAY DIFFRACTION93
4.55-5.20.16371700.13013004X-RAY DIFFRACTION94
5.2-6.550.17431660.15023045X-RAY DIFFRACTION94
6.55-100.17411460.12313163X-RAY DIFFRACTION97
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)
11.5465-0.68740.02083.20540.50671.7576-0.0631-0.1524-0.35830.34660.08560.15670.26970.0514-0.02110.28460.02890.00920.3340.0720.2988-7.16615.176116.9324
22.7226-2.6926-0.57643.16690.81740.4832-0.10190.1192-0.5490.0861-0.16250.8119-0.0725-0.19360.28120.34020.04080.01090.39720.02230.5438-30.650424.00429.6005
31.0889-0.6511-0.28772.7861.15081.89870.0103-0.02370.1659-0.09440.1015-0.1687-0.53160.1411-0.09260.3951-0.04050.03240.33120.03710.2468-4.429836.246318.4608
49.08091.2457-0.55148.31310.48046.14680.18330.6340.299-0.5188-0.1312-0.9564-0.64520.6499-0.01780.7015-0.08710.10620.47750.06660.3446-0.521642.09239.9822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 560 through 755 )
2X-RAY DIFFRACTION2chain 'A' and (resid 756 through 937 )
3X-RAY DIFFRACTION3chain 'A' and (resid 938 through 1154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1155 through 1201 )

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