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- PDB-6vsp: Structure of Serratia marcescens 2,3-butanediol dehydrogenase mut... -

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Basic information

Entry
Database: PDB / ID: 6vsp
TitleStructure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A
Components2,3-butanediol dehydrogenase
KeywordsOXIDOREDUCTASE / BDH
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Meso-2,3-butanediol dehydrogenase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Biotechnol Biofuels / Year: 2020
Title: Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression.
Authors: Subramanian, V. / Lunin, V.V. / Farmer, S.J. / Alahuhta, M. / Moore, K.T. / Ho, A. / Chaudhari, Y.B. / Zhang, M. / Himmel, M.E. / Decker, S.R.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,09215
Polymers55,7652
Non-polymers2,32713
Water9,710539
1
A: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules

A: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,18430
Polymers111,5314
Non-polymers4,65326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24550 Å2
ΔGint-159 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.675, 108.675, 82.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2,3-butanediol dehydrogenase / 3-oxoacyl-ACP reductase / SDR family oxidoreductase


Mass: 27882.711 Da / Num. of mol.: 2 / Mutation: Q247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: budC, A8A12_06140, FG174_10665 / Production host: Zymomonas mobilis (bacteria)
References: UniProt: H9XP47, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 6 types, 552 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate, pH 6-7, 6-15% w/v PEG3350 / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 16, 2017 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39724 / % possible obs: 100 % / Redundancy: 17.32 % / Rsym value: 0.1087 / Net I/σ(I): 18.67
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.58 / Num. unique obs: 5531 / Rsym value: 0.7479

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOLREPphasing
PROTEUM PLUSdata reduction
PROTEUM PLUSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6VSM

6vsm
PDB Unreleased entry


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.912 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2219 1895 4.792 %
Rwork0.1677 --
all0.17 --
obs-39547 99.665 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.012 Å2
Baniso -1Baniso -2Baniso -3
1--0.113 Å20 Å20 Å2
2---0.113 Å20 Å2
3---0.226 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 151 539 4358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134011
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173762
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6295460
X-RAY DIFFRACTIONr_angle_other_deg1.4041.5828682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73422.21181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58715622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4321526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
X-RAY DIFFRACTIONr_nbd_refined0.2280.2834
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.23583
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2409
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3870.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.244
X-RAY DIFFRACTIONr_nbd_other0.2040.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.241
X-RAY DIFFRACTIONr_mcbond_it1.9682.2972081
X-RAY DIFFRACTIONr_mcbond_other1.9642.2952080
X-RAY DIFFRACTIONr_mcangle_it2.8763.4322617
X-RAY DIFFRACTIONr_mcangle_other2.8783.4352618
X-RAY DIFFRACTIONr_scbond_it2.6312.7121930
X-RAY DIFFRACTIONr_scbond_other2.6312.7121931
X-RAY DIFFRACTIONr_scangle_it4.0063.9252843
X-RAY DIFFRACTIONr_scangle_other4.0063.9252844
X-RAY DIFFRACTIONr_lrange_it6.23229.6964627
X-RAY DIFFRACTIONr_lrange_other6.0329.1334499
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.057334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3471340.342715X-RAY DIFFRACTION99.5458
1.949-2.0030.2941420.2622668X-RAY DIFFRACTION99.8579
2.003-2.0610.331240.2352603X-RAY DIFFRACTION99.817
2.061-2.1240.2721230.2192526X-RAY DIFFRACTION99.7364
2.124-2.1940.2691290.2082449X-RAY DIFFRACTION99.6906
2.194-2.2710.2551180.1922374X-RAY DIFFRACTION99.68
2.271-2.3560.2191030.1752337X-RAY DIFFRACTION99.7547
2.356-2.4520.2461320.1752168X-RAY DIFFRACTION99.524
2.452-2.5610.243940.1592131X-RAY DIFFRACTION99.4636
2.561-2.6860.2661010.1572045X-RAY DIFFRACTION99.5824
2.686-2.8310.255970.1471933X-RAY DIFFRACTION99.8033
2.831-3.0030.228880.1391852X-RAY DIFFRACTION99.2835
3.003-3.210.166690.1461757X-RAY DIFFRACTION99.5638
3.21-3.4660.184800.1411620X-RAY DIFFRACTION99.6483
3.466-3.7960.171750.1351515X-RAY DIFFRACTION99.8117
3.796-4.2430.168800.1221358X-RAY DIFFRACTION99.8611
4.243-4.8970.169750.1131211X-RAY DIFFRACTION100
4.897-5.9920.15610.1371050X-RAY DIFFRACTION100
5.992-8.4480.195430.148832X-RAY DIFFRACTION100
8.448-500.269270.204508X-RAY DIFFRACTION99.2579

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