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- PDB-6k8w: Crystal structure of N-domain with NADP of baterial malonyl-CoA r... -

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Basic information

Entry
Database: PDB / ID: 6k8w
TitleCrystal structure of N-domain with NADP of baterial malonyl-CoA reductase
ComponentsNAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SDR domain
Function / homologyoxidoreductase 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesPorphyrobacter dokdonensis DSW-74 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsKim, S. / Kim, K.-J.
CitationJournal: Environ.Microbiol. / Year: 2020
Title: Structural insight into bi-functional malonyl-CoA reductase.
Authors: Son, H.F. / Kim, S. / Seo, H. / Hong, J. / Lee, D. / Jin, K.S. / Park, S. / Kim, K.J.
History
DepositionJun 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR
B: NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1215
Polymers122,5392
Non-polymers1,5833
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-31 kcal/mol
Surface area38560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.871, 109.114, 130.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR


Mass: 61269.301 Da / Num. of mol.: 2 / Fragment: SDR N-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyrobacter dokdonensis DSW-74 (bacteria)
Gene: I603_0811 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1A7BFR5
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Li2SO4, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.17→50 Å / Num. obs: 20735 / % possible obs: 97.4 % / Redundancy: 4.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.074 / Rsym value: 0.171 / Net I/σ(I): 13.1
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.302 / Num. unique obs: 987 / CC1/2: 0.845 / Rpim(I) all: 0.173 / Rsym value: 0.351

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K8V

6k8v


Resolution: 3.17→33.76 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.845 / SU B: 31.898 / SU ML: 0.513 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.592
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 1019 4.9 %RANDOM
Rwork0.2089 ---
obs0.2107 19703 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.07 Å2 / Biso mean: 43.266 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.07 Å2-0 Å2-0 Å2
2---2.79 Å20 Å2
3---8.86 Å2
Refinement stepCycle: final / Resolution: 3.17→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 101 25 8274
Biso mean--60.12 11.08 -
Num. residues----1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138407
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177872
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.66111426
X-RAY DIFFRACTIONr_angle_other_deg1.1721.5818157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6551090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7720.956429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.937151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0711576
X-RAY DIFFRACTIONr_chiral_restr0.0540.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029584
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021802
LS refinement shellResolution: 3.174→3.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 78 -
Rwork0.305 1246 -
all-1324 -
obs--85.53 %

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