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- PDB-6xew: Structure of Serratia marcescens 2,3-butanediol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6xew
TitleStructure of Serratia marcescens 2,3-butanediol dehydrogenase
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 / R,3-HYDROXYBUTAN-2-ONE / S,3-HYDROXYBUTAN-2-ONE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Meso-2,3-butanediol dehydrogenase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJun 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)57,8107
Polymers55,8802
Non-polymers1,9305
Water7,891438
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)115,62014
Polymers111,7594
Non-polymers3,86110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22330 Å2
ΔGint-117 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.171, 108.171, 82.881
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: 27939.762 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 443 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-HBR / R,3-HYDROXYBUTAN-2-ONE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HBS / S,3-HYDROXYBUTAN-2-ONE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.31 Å3/Da / Density % sol: 43.3 %
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: Mar 23, 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: 2→50 Å / Num. obs: 33823 / % possible obs: 100 % / Redundancy: 11.42 % / Rsym value: 0.1377 / Net I/σ(I): 11.23
Reflection shellResolution: 2→2.1 Å / Redundancy: 8.77 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 4496 / Rsym value: 0.6889 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI5

4ni5


Resolution: 2→45.335 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.525 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2141 1711 5.092 %
Rwork0.1622 31891 -
all0.165 --
obs-33602 99.503 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.405 Å20 Å20 Å2
2---0.405 Å20 Å2
3---0.809 Å2
Refinement stepCycle: LAST / Resolution: 2→45.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 127 438 4226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133935
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173666
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.6275370
X-RAY DIFFRACTIONr_angle_other_deg1.4411.5838462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34622.402179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58215608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0481525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
X-RAY DIFFRACTIONr_nbd_refined0.2120.2830
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23519
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21934
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2327
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.241
X-RAY DIFFRACTIONr_nbd_other0.2020.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.242
X-RAY DIFFRACTIONr_mcbond_it1.8472.3212050
X-RAY DIFFRACTIONr_mcbond_other1.8462.3182049
X-RAY DIFFRACTIONr_mcangle_it2.6843.472573
X-RAY DIFFRACTIONr_mcangle_other2.6843.4722574
X-RAY DIFFRACTIONr_scbond_it2.5862.7181885
X-RAY DIFFRACTIONr_scbond_other2.5852.7181886
X-RAY DIFFRACTIONr_scangle_it4.0113.9482797
X-RAY DIFFRACTIONr_scangle_other4.0113.9482798
X-RAY DIFFRACTIONr_lrange_it5.64629.614498
X-RAY DIFFRACTIONr_lrange_other5.47829.1824406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3781180.2792278X-RAY DIFFRACTION98.7227
2.052-2.1080.2671050.2612263X-RAY DIFFRACTION99.3289
2.108-2.1690.2841250.2312204X-RAY DIFFRACTION99.1908
2.169-2.2360.2771360.2182117X-RAY DIFFRACTION99.8228
2.236-2.3090.2481070.1972079X-RAY DIFFRACTION99.3185
2.309-2.390.251010.1832018X-RAY DIFFRACTION99.2506
2.39-2.480.2781030.1831943X-RAY DIFFRACTION99.8049
2.48-2.5820.2881040.1891867X-RAY DIFFRACTION99.2947
2.582-2.6960.2541030.1581776X-RAY DIFFRACTION99.208
2.696-2.8280.21780.1591744X-RAY DIFFRACTION99.5628
2.828-2.980.2141050.1481631X-RAY DIFFRACTION99.7128
2.98-3.1610.158870.1391566X-RAY DIFFRACTION99.6383
3.161-3.3790.158840.1321465X-RAY DIFFRACTION99.7424
3.379-3.6490.162690.1211392X-RAY DIFFRACTION99.6589
3.649-3.9960.169670.1151288X-RAY DIFFRACTION99.9263
3.996-4.4660.156580.1071164X-RAY DIFFRACTION100
4.466-5.1540.151420.1271061X-RAY DIFFRACTION100
5.154-6.3050.227470.176897X-RAY DIFFRACTION100
6.305-8.8870.175420.142709X-RAY DIFFRACTION100
8.887-45.3350.214300.19429X-RAY DIFFRACTION98.9224

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