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- PDB-8j2b: Structure of the C-terminal subenzyme of the malonyl-CoA reductas... -

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Basic information

Entry
Database: PDB / ID: 8j2b
TitleStructure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, in complex with NADP+ and malonate
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / 3-hydroxypropionate(3-HP) / malonyl-CoA reductase / CO2 fixation / short-chain dehydrogenase/reductase (SDR) / Chloroflexus aurantiacus
Function / homology
Function and homology information


fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding
Similarity search - Function
short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
MALONIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)74,4993
Polymers73,6521
Non-polymers8472
Water2,108117
1
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9996
Polymers147,3042
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area9040 Å2
ΔGint-51 kcal/mol
Surface area45200 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.960, 125.220, 73.810
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number5
Space group name H-MC121

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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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with NADP+ and malonate was obtained by crystallizing in drops containing 1.5 ul protein solution (10 mg/ml protein+1.7 mM NADP disodium salt, incubated at 4 degrees ...Details: The protein in complex with NADP+ and malonate was obtained by crystallizing 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 (250 mM sodium malonate pH 7.0, 10% w/v PEG 6000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97906 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.127→62.612 Å / Num. obs: 48013 / % possible obs: 96.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Rsym value: 0.055 / Net I/σ(I): 17.7
Reflection shellResolution: 2.127→2.163 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2428 / CC1/2: 0.793 / Rpim(I) all: 0.289 / Rrim(I) all: 0.784 / Rsym value: 0.728 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSJan 26, 2018 (BUILT 20180409)data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→62.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.167 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2377 4.97 %RANDOM
Rwork0.185 ---
obs0.186 47800 96.9 %-
Displacement parametersBiso mean: 60.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.815 Å20 Å2-0.3461 Å2
2--1.2072 Å20 Å2
3---2.6079 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.13→62.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 55 117 5212
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015192HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.057052HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1824SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes794HARMONIC5
X-RAY DIFFRACTIONt_it5192HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion685SEMIHARMONIC5
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_contact6045SEMIHARMONIC4
LS refinement shellResolution: 2.13→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 183 5.15 %
Rwork0.19 3367 -
all0.19 3550 -
obs--97.6 %
Refinement TLS params.Method: refined / Origin x: -47.9909 Å / Origin y: 7.1827 Å / Origin z: 21.2017 Å
111213212223313233
T-0.2074 Å20.0076 Å2-0.0043 Å2--0.1661 Å2-0.0527 Å2---0.2579 Å2
L0.5264 °20.2786 °2-0.2127 °2-1.483 °2-0.7713 °2--1.4139 °2
S-0.02 Å °0.0495 Å °-0.1096 Å °-0.0426 Å °0.0421 Å °-0.1486 Å °-0.1508 Å °-0.0502 Å °-0.0221 Å °
Refinement TLS groupSelection details: { A|562 - A|1219 }

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