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- PDB-3e9m: Crystal Structure of an oxidoreductase from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 3e9m
TitleCrystal Structure of an oxidoreductase from Enterococcus faecalis
ComponentsOxidoreductase, Gfo/Idh/MocA family
KeywordsOXIDOREDUCTASE / Gfo/ldh/MocA / PSI-II / 11133d1 / Dimeric Dihydodiol Dehydrogenase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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 ...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
Oxidoreductase, Gfo/Idh/MocA family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of an oxidoreductase from Enterococcus faecalis
Authors: Damodharan, L. / K Burley, S.K. / Swaminathan, S.
History
DepositionAug 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
C: Oxidoreductase, Gfo/Idh/MocA family
D: Oxidoreductase, Gfo/Idh/MocA family


Theoretical massNumber of molelcules
Total (without water)148,5884
Polymers148,5884
Non-polymers00
Water0
1
A: Oxidoreductase, Gfo/Idh/MocA family
D: Oxidoreductase, Gfo/Idh/MocA family


Theoretical massNumber of molelcules
Total (without water)74,2942
Polymers74,2942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-20 kcal/mol
Surface area26390 Å2
MethodPISA
2
B: Oxidoreductase, Gfo/Idh/MocA family

C: Oxidoreductase, Gfo/Idh/MocA family


Theoretical massNumber of molelcules
Total (without water)74,2942
Polymers74,2942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2670 Å2
ΔGint-23 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.918, 146.925, 80.531
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological assembly is a dimer of dimer.

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Components

#1: Protein
Oxidoreductase, Gfo/Idh/MocA family /


Mass: 37147.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_0827 / Plasmid: PSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q837L0

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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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% polyethylene Glycol Monomethyl ether 2000, 0.1M Bis-Tris., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2008 / Details: mirrors
RadiationMonochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 37176 / Num. obs: 37176 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 4411 / % possible all: 76.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXD& SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→37.12 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 94842.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1664 5.1 %RANDOM
Rwork0.233 ---
all0.269 32882 --
obs0.233 32882 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.2933 Å2 / ksol: 0.315491 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å25.96 Å2
2---8.24 Å20 Å2
3---4.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9967 0 0 0 9967
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 243 5.2 %
Rwork0.305 4411 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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