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- PDB-4ew6: Crystal structure of D-galactose-1-dehydrogenase protein from Rhi... -

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Basic information

Entry
Database: PDB / ID: 4ew6
TitleCrystal structure of D-galactose-1-dehydrogenase protein from Rhizobium etli
ComponentsD-galactose-1-dehydrogenase protein
KeywordsOXIDOREDUCTASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / two domain / GFO/IDH/MOCA family
Function / homology
Function and homology information


D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / nucleotide binding
Similarity search - Function
: / 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
D-galactose-1-dehydrogenase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsEswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of D-galactose-1-dehydrogenase protein from Rhizobium etli
Authors: Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-galactose-1-dehydrogenase protein


Theoretical massNumber of molelcules
Total (without water)36,5961
Polymers36,5961
Non-polymers00
Water90150
1
A: D-galactose-1-dehydrogenase protein

A: D-galactose-1-dehydrogenase protein


Theoretical massNumber of molelcules
Total (without water)73,1932
Polymers73,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2720 Å2
ΔGint-26 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.109, 52.109, 265.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein D-galactose-1-dehydrogenase protein


Mass: 36596.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: gal, RHE_CH01458 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2KA75, D-galactose 1-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium Acetate, 0.1M Tris HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 17360 / Num. obs: 17360 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.5 % / Rmerge(I) obs: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.9 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.95 / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29331 870 5.1 %RANDOM
Rwork0.24364 ---
obs0.24612 16312 98.96 %-
all-16312 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 50 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9373320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74723.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84115376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8811513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.881.51540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63422467
X-RAY DIFFRACTIONr_scbond_it2.5273899
X-RAY DIFFRACTIONr_scangle_it4.0344.5853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 67 -
Rwork0.25 1160 -
obs--99.59 %

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