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- PDB-8a30: Malonyl-CoA reductase from Chloroflexus aurantiacus - C-terminal Apo -

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Basic information

Entry
Database: PDB / ID: 8a30
TitleMalonyl-CoA reductase from Chloroflexus aurantiacus - C-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 / 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: 1.45 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 6, 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

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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)73,3462
Polymers73,3211
Non-polymers241
Water11,115617
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,6924
Polymers146,6432
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6230 Å2
ΔGint-43 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.138, 140.181, 74.026
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1441-

HOH

21A-1567-

HOH

31A-1683-

HOH

41A-1974-

HOH

51A-1989-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M Succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.45→55.5 Å / Num. obs: 154410 / % possible obs: 99.36 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.09 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04132 / Rpim(I) all: 0.04132 / Rrim(I) all: 0.05843 / Net I/av σ(I): 9.93 / Net I/σ(I): 10.6
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.441 / Num. unique obs: 15025 / CC1/2: 0.203 / CC star: 0.581

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Processing

Software
NameVersionClassification
REFMAC(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→55.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 14408 4.99 %7654
Rwork0.1763 ---
obs0.1775 153739 94.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 1 617 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055172
X-RAY DIFFRACTIONf_angle_d0.7627026
X-RAY DIFFRACTIONf_dihedral_angle_d11.4721933
X-RAY DIFFRACTIONf_chiral_restr0.069799
X-RAY DIFFRACTIONf_plane_restr0.006931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.43694270.43347541X-RAY DIFFRACTION78
1.47-1.480.41684310.41378437X-RAY DIFFRACTION86
1.48-1.50.40414330.39988705X-RAY DIFFRACTION88
1.5-1.520.38585060.38338755X-RAY DIFFRACTION91
1.52-1.540.3754490.3759156X-RAY DIFFRACTION94
1.54-1.560.3984840.35889223X-RAY DIFFRACTION94
1.56-1.580.36235090.3529170X-RAY DIFFRACTION94
1.58-1.610.3374850.32959001X-RAY DIFFRACTION94
1.61-1.630.38264200.32419106X-RAY DIFFRACTION93
1.63-1.660.33154370.30578976X-RAY DIFFRACTION92
1.66-1.690.30614440.29049329X-RAY DIFFRACTION95
1.69-1.720.30684370.27849200X-RAY DIFFRACTION94
1.72-1.750.29924770.26489066X-RAY DIFFRACTION94
1.75-1.790.28094810.26159421X-RAY DIFFRACTION96
1.79-1.830.25445210.24299321X-RAY DIFFRACTION96
1.83-1.870.26854580.21669334X-RAY DIFFRACTION96
1.87-1.920.21944660.20039231X-RAY DIFFRACTION95
1.92-1.970.21255070.18529026X-RAY DIFFRACTION93
1.97-2.030.19335560.17089321X-RAY DIFFRACTION96
2.03-2.090.1815560.16669156X-RAY DIFFRACTION95
2.09-2.170.2124840.16039441X-RAY DIFFRACTION97
2.17-2.250.16885040.15169369X-RAY DIFFRACTION97
2.25-2.350.17244890.14639468X-RAY DIFFRACTION96
2.36-2.480.17024690.15079098X-RAY DIFFRACTION94
2.48-2.630.19024230.14939462X-RAY DIFFRACTION97
2.63-2.840.18454810.15579386X-RAY DIFFRACTION96
2.84-3.120.20595580.15779486X-RAY DIFFRACTION98
3.12-3.580.17334620.14329394X-RAY DIFFRACTION96
3.58-4.50.14695230.11519373X-RAY DIFFRACTION97
4.5-100.13245310.12549539X-RAY DIFFRACTION98
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)
10.5047-0.3129-0.01081.60010.4040.5468-0.037-0.058-0.13250.14680.00030.09290.07750.01330.04020.16250.0092-0.00520.20540.0360.117-6.026811.939416.6114
23.25340.47460.79852.76570.70792.71750.0028-0.16910.00380.14020.05980.17810.0109-0.0702-0.03660.12380.03870.00530.1695-0.00130.1064-35.842.783614.7237
30.2362-0.0611-0.13740.8380.29880.5280.01290.02020.0038-0.0358-0.0041-0.0236-0.15720.0306-0.00810.22450.0051-0.02610.25160.01350.0881-4.292340.087314.2401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 782 )A561 - 782
2X-RAY DIFFRACTION2chain 'A' and (resid 783 through 898 )A783 - 898
3X-RAY DIFFRACTION3chain 'A' and (resid 899 through 1219 )A899 - 1219

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