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- PDB-6csj: Structure of a Bacillus coagulans polyol dehydrogenase double mut... -

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Basic information

Entry
Database: PDB / ID: 6csj
TitleStructure of a Bacillus coagulans polyol dehydrogenase double mutant with an acquired D-lactate dehydrogenase activity
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / polyol dehydrogenase
Function / homology
Function and homology information


glycerol dehydrogenase (NAD+) activity / glycerol dehydrogenase / metal ion binding
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycerol dehydrogenase
Similarity search - Component
Biological speciesBacillus coagulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 Å
AuthorsHurlbert, J.C. / St.John, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5 P20 RR16461 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Kinetic characterization and structure analysis of an altered polyol dehydrogenase with d-lactate dehydrogenase activity.
Authors: Chauliac, D. / Wang, Q. / St John, F.J. / Jones, G. / Hurlbert, J.C. / Ingram, L.O. / Shanmugam, K.T.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
C: Glycerol dehydrogenase
D: Glycerol dehydrogenase
E: Glycerol dehydrogenase
F: Glycerol dehydrogenase
G: Glycerol dehydrogenase
H: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)314,8968
Polymers314,8968
Non-polymers00
Water9,044502
1
A: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glycerol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,3621
Polymers39,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.672, 211.772, 149.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Glycerol dehydrogenase


Mass: 39361.973 Da / Num. of mol.: 8 / Mutation: D121N, F245S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coagulans (bacteria) / Gene: ldhA / Plasmid: pET15b / Production host: Escherichia coli Rosetta(DE3) (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A150JSL8, glycerol dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.2M Ammonium citrate dibasic, 10% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014 / Details: Sagittal focusing 2nd crystal horizontal focusing
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→149.71 Å / Num. obs: 126258 / % possible obs: 96.07 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.148 / Χ2: 1.105 / Net I/av σ(I): 11.641 / Net I/σ(I): 5.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6252 / CC1/2: 0.904 / Rpim(I) all: 0.21 / Rrim(I) all: 0.539 / Χ2: 0.81 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ3

1kq3


Resolution: 2.395→149.71 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.208 / SU B: 10.698 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 6235 4.938 %RANDOM
Rwork0.2374 120023 --
all0.239 ---
obs-126258 96.071 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.388 Å2
Baniso -1Baniso -2Baniso -3
1--1.451 Å20 Å20 Å2
2---2.035 Å20 Å2
3---3.485 Å2
Refinement stepCycle: LAST / Resolution: 2.395→149.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22070 0 0 502 22572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01922430
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221520
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.98430384
X-RAY DIFFRACTIONr_angle_other_deg0.918350004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53952920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28525.238840
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.604153940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3241572
X-RAY DIFFRACTIONr_chiral_restr0.0720.23592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024128
X-RAY DIFFRACTIONr_nbd_refined0.1890.28896
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1350.240142
X-RAY DIFFRACTIONr_nbtor_refined0.160.222468
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.220918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21352
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.237
X-RAY DIFFRACTIONr_nbd_other0.1790.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2770.210
X-RAY DIFFRACTIONr_mcbond_it2.7022.52411704
X-RAY DIFFRACTIONr_mcbond_other2.7012.52411703
X-RAY DIFFRACTIONr_mcangle_it3.943.78314616
X-RAY DIFFRACTIONr_mcangle_other3.943.78314617
X-RAY DIFFRACTIONr_scbond_it3.9583.01210722
X-RAY DIFFRACTIONr_scbond_other3.9583.01210723
X-RAY DIFFRACTIONr_scangle_it5.9214.31715766
X-RAY DIFFRACTIONr_scangle_other5.9214.31715767
X-RAY DIFFRACTIONr_lrange_it6.96830.6424857
X-RAY DIFFRACTIONr_lrange_other6.9730.64224809
X-RAY DIFFRACTIONr_ncsr_local_group_10.0290.0523270
X-RAY DIFFRACTIONr_ncsr_local_group_20.0330.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_30.0460.0523184
X-RAY DIFFRACTIONr_ncsr_local_group_40.030.0523306
X-RAY DIFFRACTIONr_ncsr_local_group_50.0460.0523162
X-RAY DIFFRACTIONr_ncsr_local_group_60.0470.0523128
X-RAY DIFFRACTIONr_ncsr_local_group_70.0460.0523094
X-RAY DIFFRACTIONr_ncsr_local_group_80.0310.0523250
X-RAY DIFFRACTIONr_ncsr_local_group_90.0470.0523160
X-RAY DIFFRACTIONr_ncsr_local_group_100.0360.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_110.0440.0523114
X-RAY DIFFRACTIONr_ncsr_local_group_120.0470.0523164
X-RAY DIFFRACTIONr_ncsr_local_group_130.0490.0523070
X-RAY DIFFRACTIONr_ncsr_local_group_140.0440.0523162
X-RAY DIFFRACTIONr_ncsr_local_group_150.0320.0523250
X-RAY DIFFRACTIONr_ncsr_local_group_160.0420.0523098
X-RAY DIFFRACTIONr_ncsr_local_group_170.0460.0523116
X-RAY DIFFRACTIONr_ncsr_local_group_180.0430.0523050
X-RAY DIFFRACTIONr_ncsr_local_group_190.0450.0523200
X-RAY DIFFRACTIONr_ncsr_local_group_200.0310.0523276
X-RAY DIFFRACTIONr_ncsr_local_group_210.0360.0523292
X-RAY DIFFRACTIONr_ncsr_local_group_220.0270.0523320
X-RAY DIFFRACTIONr_ncsr_local_group_230.0460.0523122
X-RAY DIFFRACTIONr_ncsr_local_group_240.0480.0523172
X-RAY DIFFRACTIONr_ncsr_local_group_250.0450.0523098
X-RAY DIFFRACTIONr_ncsr_local_group_260.0330.0523260
X-RAY DIFFRACTIONr_ncsr_local_group_270.0270.0523244
X-RAY DIFFRACTIONr_ncsr_local_group_280.0360.0523194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
2.395-2.4570.3464340.31282510.313970289.51760.254
2.457-2.5240.3614850.31386610.315934997.82860.259
2.524-2.5980.3414210.29285450.294915597.93560.238
2.598-2.6770.3033620.27783750.278893197.82780.226
2.677-2.7650.2844320.26479190.265855997.56980.215
2.765-2.8620.2924430.2576960.253834397.55480.205
2.862-2.970.2853740.23874340.24802497.30810.195
2.97-3.0910.2723620.24571690.247775597.11150.207
3.091-3.2290.2993570.23768620.24744297.00350.209
3.229-3.3860.2723770.23665110.238712296.71440.213
3.386-3.5690.2422820.22662830.227680996.41650.206
3.569-3.7860.2432560.22459370.225642796.35910.208
3.786-4.0470.2262570.20755490.208605695.87190.195
4.047-4.3710.2172880.19850840.199561595.67230.189
4.371-4.7880.2432570.19947360.201523395.41370.193
4.788-5.3520.2242410.20742210.208470694.81510.198
5.352-6.1790.2591570.22838070.229419194.58360.214
6.179-7.5650.2092320.19331240.194358093.7430.188
7.565-10.6840.2051160.18324900.184280293.0050.193
10.684-149.710.3341020.28113690.284162190.74650.292

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