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- PDB-3ezy: Crystal structure of probable dehydrogenase TM_0414 from Thermoto... -

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Basic information

Entry
Database: PDB / ID: 3ezy
TitleCrystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima
ComponentsDehydrogenase
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


inositol 2-dehydrogenase / inositol 2-dehydrogenase (NAD+) activity / NADPH regeneration / inositol metabolic process / oxidoreductase activity / cytoplasm
Similarity search - Function
Inositol 2-dehydrogenase / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Inositol 2-dehydrogenase / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Myo-inositol 2-dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å
AuthorsRamagopal, U.A. / Toro, R. / Freeman, J. / Chang, S. / Maletic, M. / Gheyi, T. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima
Authors: Ramagopal, U.A. / Toro, R. / Freeman, J. / Chang, S. / Maletic, M. / Gheyi, T. / Burley, S.K. / Almo, S.C.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dehydrogenase
B: Dehydrogenase
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,6169
Polymers155,0254
Non-polymers5915
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-96 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.144, 108.739, 98.496
Angle α, β, γ (deg.)90.00, 96.26, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asymmetric unit.

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Components

#1: Protein
Dehydrogenase /


Mass: 38756.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0414 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYP5
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% MPD, Bis-Tris pH 6.5, 0.1M Calcium Chloride, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 91568 / Num. obs: 91568 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.074 / Χ2: 1.032 / Net I/σ(I): 17.16
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.51 / Num. unique all: 18000 / Rsym value: 0.577 / Χ2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
HKL2Mapphasing
RefinementResolution: 2.04→42.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.859 / SU B: 4.187 / SU ML: 0.117 / SU R Cruickshank DPI: 0.188 / SU Rfree: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4565 5 %RANDOM
Rwork0.175 ---
obs0.177 91498 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.6 Å2 / Biso mean: 32.677 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-1.51 Å2
2---1 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.04→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10577 0 24 616 11217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210787
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.98614540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78551356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80523.728507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.382152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3461597
X-RAY DIFFRACTIONr_chiral_restr0.1120.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218033
X-RAY DIFFRACTIONr_mcbond_it0.8311.56625
X-RAY DIFFRACTIONr_mcangle_it1.578210703
X-RAY DIFFRACTIONr_scbond_it2.82734162
X-RAY DIFFRACTIONr_scangle_it4.7414.53820
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 300 -
Rwork0.219 5969 -
all-6269 -
obs--92.79 %

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