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- PDB-8j29: Structures of the C-terminal subenzyme of the malonyl-CoA reducta... -

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Entry
Database: PDB / ID: 8j29
TitleStructures of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / 3-hydroxypropionate(3-HP) / malonyl-CoA reductase / CO2 fixation / short-chain dehydrogenase/reductase (SDR) / Chloroflexus aurantiacus
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 / L(+)-TARTARIC ACID / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMa, Q. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)xxxx China
CitationJournal: To Be Published
Title: Structures of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus
Authors: Ma, Q. / Liu, C.
History
DepositionApr 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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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)73,8943
Polymers73,6521
Non-polymers2422
Water6,161342
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7886
Polymers147,3042
Non-polymers4844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area7310 Å2
ΔGint-21 kcal/mol
Surface area46180 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-0 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.410, 139.460, 73.870
Angle α, β, γ (deg.)90.00, 98.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2163-

HOH

21A-2186-

HOH

31A-2424-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 73651.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Gene: Caur_2614 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9WIU3
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein was crystallized in drops containing 1.5 ul protein solution (10 mg/ml) and 1.5 ul reservoir solution (900 mM ammonium tartrate pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.877→72.902 Å / Num. obs: 68842 / % possible obs: 97.7 % / Redundancy: 7 % / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Net I/σ(I): 21.9
Reflection shellResolution: 1.877→1.883 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 657 / CC1/2: 0.877 / Rpim(I) all: 0.282 / Rrim(I) all: 0.76 / Rsym value: 0.705 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSJan 26, 2018, built on 20180409data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→27.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3400 4.97 %RANDOM
Rwork0.176 ---
obs0.177 68471 97.7 %-
Displacement parametersBiso mean: 38.69 Å2
Baniso -1Baniso -2Baniso -3
1--9.2189 Å20 Å24.219 Å2
2--3.6959 Å20 Å2
3---5.523 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.88→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 16 342 5358
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956947HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1797SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes768HARMONIC5
X-RAY DIFFRACTIONt_it5119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion15.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion678SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6244SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 261 5.19 %
Rwork0.208 4770 -
all0.21 5031 -
obs--97.85 %
Refinement TLS params.Method: refined / Origin x: -0.3265 Å / Origin y: 71.5753 Å / Origin z: 57.9217 Å
111213212223313233
T-0.0411 Å2-0.0072 Å2-0.0132 Å2--0.0732 Å2-0.0135 Å2---0.1139 Å2
L0.2594 °20.1418 °2-0.0529 °2-0.7833 °2-0.1539 °2--0.3836 °2
S-0.0084 Å °0.0154 Å °-0.045 Å °-0.02 Å °0.0035 Å °-0.0674 Å °-0.0573 Å °-0.0184 Å °0.0049 Å °
Refinement TLS groupSelection details: { A|561 - A|1219 }

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