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- PDB-8j2a: Structure of the C-terminal subenzyme of the malonyl-CoA reductas... -

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Basic information

Entry
Database: PDB / ID: 8j2a
TitleStructure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, 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: 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)74,5124
Polymers73,6521
Non-polymers8603
Water8,143452
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0238
Polymers147,3042
Non-polymers1,7206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area9500 Å2
ΔGint-47 kcal/mol
Surface area45530 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.990, 139.940, 73.910
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2337-

HOH

21A-2533-

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-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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 452 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
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 (15 mg/ml protein+2.6 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 (15 mg/ml protein+2.6 mM NADP disodium salt, incubated at 4 degrees for 1 h) and 1.5 ul reservoir solution (100 mM HEPES pH 7.0, 20% w/v poly(acrylic acid sodium) 5100, 5 mM MgCl2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.696→69.968 Å / Num. obs: 95052 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Rsym value: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 1.696→1.726 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4737 / CC1/2: 0.858 / Rpim(I) all: 0.32 / Rrim(I) all: 0.853 / Rsym value: 0.79 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSJan 26, 2018, built on 20180409data reduction
Aimlessversion 0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4753 5.03 %RANDOM
Rwork0.171 ---
obs0.172 94410 98.7 %-
Displacement parametersBiso mean: 32.76 Å2
Baniso -1Baniso -2Baniso -3
1--6.6851 Å20 Å23.4278 Å2
2--3.1369 Å20 Å2
3---3.5482 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 55 452 5578
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015273HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.947172HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1870SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes813HARMONIC5
X-RAY DIFFRACTIONt_it5273HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion15.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion698SEMIHARMONIC5
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_contact6522SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 352 5.06 %
Rwork0.206 6608 -
all0.207 6960 -
obs--98.47 %
Refinement TLS params.Method: refined / Origin x: -0.5021 Å / Origin y: 71.2491 Å / Origin z: 58.0139 Å
111213212223313233
T-0.0418 Å2-0.0146 Å2-0.0143 Å2--0.0627 Å2-0.0119 Å2---0.078 Å2
L0.2398 °20.0604 °2-0.0829 °2-0.5262 °2-0.1132 °2--0.2795 °2
S-0.0102 Å °0.0201 Å °-0.0378 Å °-0.0442 Å °-0.0061 Å °-0.0445 Å °-0.0461 Å °-0.0098 Å °0.0163 Å °
Refinement TLS groupSelection details: { A|562 - A|1219 }

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