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

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Basic information

Entry
Database: PDB / ID: 8aet
TitleMalonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal E779W 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 / 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: 2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,8596
Polymers73,3791
Non-polymers4805
Water6,593366
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,71812
Polymers146,7572
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8340 Å2
ΔGint-190 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.167, 139.643, 73.306
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1552-

HOH

21A-1753-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 73378.547 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate, pH 6.5, 1.4 M Sodium acetate trihydrate

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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: 2→50.3 Å / Num. obs: 112286 / % possible obs: 97.93 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.24 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05477 / Rpim(I) all: 0.05477 / Rrim(I) all: 0.07746 / Net I/σ(I): 7.41
Reflection shellResolution: 2→2.072 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4288 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 10828 / CC1/2: 0.691 / CC star: 0.904 / Rpim(I) all: 0.4288 / Rrim(I) all: 0.6064 / % possible all: 96.69

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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→50.3 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2898 5.06 %
Rwork0.1905 --
obs0.192 57248 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 25 366 5375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065097
X-RAY DIFFRACTIONf_angle_d0.8036920
X-RAY DIFFRACTIONf_dihedral_angle_d12.5941897
X-RAY DIFFRACTIONf_chiral_restr0.046787
X-RAY DIFFRACTIONf_plane_restr0.007910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30581200.25952251X-RAY DIFFRACTION85
2.03-2.060.29181450.25182645X-RAY DIFFRACTION100
2.06-2.10.25271340.23152632X-RAY DIFFRACTION100
2.1-2.140.24991560.2172599X-RAY DIFFRACTION100
2.14-2.190.24181470.22262649X-RAY DIFFRACTION100
2.19-2.230.51551260.43882323X-RAY DIFFRACTION88
2.23-2.290.5591020.48442109X-RAY DIFFRACTION78
2.29-2.340.26531510.20882599X-RAY DIFFRACTION100
2.34-2.410.23621370.18982652X-RAY DIFFRACTION100
2.41-2.480.2371460.18342621X-RAY DIFFRACTION100
2.48-2.560.21651530.18732644X-RAY DIFFRACTION100
2.56-2.650.21871290.18062687X-RAY DIFFRACTION100
2.65-2.750.18071090.17862658X-RAY DIFFRACTION100
2.75-2.880.20921250.1812645X-RAY DIFFRACTION100
2.88-3.030.23841540.18672666X-RAY DIFFRACTION100
3.03-3.220.23591310.1952656X-RAY DIFFRACTION100
3.22-3.470.19931330.17152673X-RAY DIFFRACTION100
3.47-3.820.20351550.17472617X-RAY DIFFRACTION99
3.82-4.370.16451300.14412687X-RAY DIFFRACTION100
4.37-5.510.1491660.1492642X-RAY DIFFRACTION100
5.51-100.20031490.16252695X-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)
10.9798-0.6149-0.00283.03320.71990.8701-0.0362-0.0339-0.17610.1218-0.01030.15830.07570.02570.04660.18560.02040.02260.22410.03180.2007-5.629712.089916.8447
23.48350.0211.29451.51860.27452.9711-0.039-0.1506-0.02860.16690.07870.3321-0.0477-0.0985-0.01370.17980.05560.02580.1637-0.01350.2877-35.835443.37314.8122
30.3903-0.071-0.10931.28090.44140.97520.00220.09060.019-0.0741-0.0129-0.0213-0.25220.06340.0010.23410.00140.00010.24050.0190.1479-4.268440.043114.0323
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 1219 )

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