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- PDB-8j2d: Structure of the C-terminal subenzyme of the malonyl-CoA reductas... -

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Basic information

Entry
Database: PDB / ID: 8j2d
TitleStructure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, mutant N940V/K1106W/S1114R in complex with NADP+
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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)74,6003
Polymers73,7641
Non-polymers8352
Water2,000111
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1996
Polymers147,5282
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area9280 Å2
ΔGint-38 kcal/mol
Surface area44130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-4 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.220, 126.010, 73.440
Angle α, β, γ (deg.)90.00, 102.33, 90.00
Int Tables number5
Space group name H-MC121

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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-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-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.: 111 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with NADP+ was crystallized in drops containing 1.5 ul protein solution (10 mg/ml protein+1.7 mM NADP disodium salt, incubated at 4 degrees for 1 h) and 1.5 ul ...Details: The protein in complex with NADP+ was crystallized in drops containing 1.5 ul protein solution (10 mg/ml protein+1.7 mM NADP disodium salt, incubated at 4 degrees for 1 h) and 1.5 ul reservoir solution (100 mM sodium citrate pH 5.0, 150 mM sodium citrate, 16% w/v PEG3350).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.205→75.846 Å / Num. obs: 43280 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Rsym value: 0.077 / Net I/σ(I): 13.6
Reflection shellResolution: 2.205→2.243 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2146 / CC1/2: 0.841 / Rpim(I) all: 0.318 / Rrim(I) all: 0.847 / Rsym value: 0.785 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSMar 15, 2019 (BUILT 20190315)data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→32.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2133 4.97 %RANDOM
Rwork0.193 ---
obs0.195 42959 99.5 %-
Displacement parametersBiso mean: 58.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.1367 Å20 Å20.8374 Å2
2---2.3835 Å20 Å2
3---7.5202 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.21→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 54 111 5127
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.076960HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1794SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes780HARMONIC5
X-RAY DIFFRACTIONt_it5119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion17.51
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_contact5970SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 163 5.17 %
Rwork0.193 2992 -
all0.194 3155 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -37.4451 Å / Origin y: 7.7494 Å / Origin z: -14.6344 Å
111213212223313233
T-0.1024 Å2-0.0245 Å2-0.0172 Å2--0.081 Å2-0.027 Å2---0.1831 Å2
L0.4857 °20.1858 °2-0.0504 °2-1.254 °2-0.3159 °2--0.9716 °2
S0.0063 Å °0.0327 Å °-0.0969 Å °-0.0425 Å °-0.0023 Å °-0.1534 Å °-0.1564 Å °0.0355 Å °-0.004 Å °
Refinement TLS groupSelection details: { A|562 - A|1219 }

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