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- PDB-8j2c: Structure of the C-terminal subenzyme of the malonyl-CoA reductas... -

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Basic information

Entry
Database: PDB / ID: 8j2c
TitleStructure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, mutant N940V/K1106W/S1114R
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: 1.7 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)74,0063
Polymers73,7641
Non-polymers2422
Water9,422523
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0126
Polymers147,5282
Non-polymers4844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area7700 Å2
ΔGint-23 kcal/mol
Surface area45360 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-0 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.273, 133.029, 74.119
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2248-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 73764.039 Da / Num. of mol.: 1 / Mutation: N940V/K1106W/S1114R
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.: 523 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein was crystallized in drops containing 1.5 ul protein solution (5 mg/ml) and 1.5 ul reservoir solution (1.1 M ammonium tartrate pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.697→73.265 Å / Num. obs: 91959 / % possible obs: 98.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Rsym value: 0.058 / Net I/σ(I): 17.3
Reflection shellResolution: 1.697→1.702 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 734 / CC1/2: 0.815 / Rpim(I) all: 0.277 / Rrim(I) all: 0.674 / Rsym value: 0.612 / % possible all: 76.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSversion (Nov 1, 2016, built on 20170215data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→73.265 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4565 4.98 %RANDOM
Rwork0.169 ---
obs0.17 91578 98.3 %-
Displacement parametersBiso mean: 30.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.0093 Å20 Å21.1052 Å2
2--1.8634 Å20 Å2
3---0.1458 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.7→73.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 16 523 5544
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015133HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936971HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1799SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes772HARMONIC5
X-RAY DIFFRACTIONt_it5133HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion15.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion679SEMIHARMONIC5
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_contact6629SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 271 4.82 %
Rwork0.205 5356 -
all0.206 5627 -
obs--82.14 %
Refinement TLS params.Method: refined / Origin x: -33.728 Å / Origin y: 6.8011 Å / Origin z: -14.9176 Å
111213212223313233
T-0.0673 Å2-0.0264 Å20.0019 Å2--0.0639 Å2-0.0172 Å2---0.092 Å2
L0.4271 °20.041 °20.0552 °2-0.406 °2-0.0977 °2--0.3998 °2
S-0.0121 Å °0.0178 Å °-0.0993 Å °-0.0166 Å °0.0005 Å °-0.0767 Å °-0.0661 Å °0.0036 Å °0.0116 Å °
Refinement TLS groupSelection details: { A|562 - A|1219 }

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