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- PDB-3ic5: N-terminal domain of putative saccharopine dehydrogenase from Rue... -

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Basic information

Entry
Database: PDB / ID: 3ic5
TitleN-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.
Componentsputative saccharopine dehydrogenase
Keywordsstructural genomics / unknown function / APC63807.2 / N-terminal domain / saccharopine dehydrogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine dehydrogenase
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsOsipiuk, J. / Tesar, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of N-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.
Authors: Osipiuk, J. / Tesar, C. / Freeman, L. / Joachimiak, A.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative saccharopine dehydrogenase
B: putative saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)24,6032
Polymers24,6032
Non-polymers00
Water2,126118
1
A: putative saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)12,3021
Polymers12,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)12,3021
Polymers12,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.368, 57.803, 73.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsputative biological unit is a monomer

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Components

#1: Protein putative saccharopine dehydrogenase


Mass: 12301.582 Da / Num. of mol.: 2 / Fragment: N-terminal domain 1-115 / Mutation: A110V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO0234 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LX24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris buffer, 20% ethanol, 5% PEG-400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→45.4 Å / Num. all: 14419 / Num. obs: 14419 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.085 / Χ2: 2.457 / Net I/σ(I): 12.7
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 3.22 / Num. unique all: 691 / Χ2: 1.649 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→45.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 11.678 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 722 5 %RANDOM
Rwork0.195 ---
all0.197 14349 --
obs0.197 14349 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.8 Å2 / Biso mean: 28.092 Å2 / Biso min: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2--0.08 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 118 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221724
X-RAY DIFFRACTIONr_bond_other_d0.0010.021087
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9492348
X-RAY DIFFRACTIONr_angle_other_deg0.95132690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38525.16162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87115281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.981156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
X-RAY DIFFRACTIONr_mcbond_it0.8431.51157
X-RAY DIFFRACTIONr_mcbond_other0.2281.5477
X-RAY DIFFRACTIONr_mcangle_it1.46521835
X-RAY DIFFRACTIONr_scbond_it2.4083567
X-RAY DIFFRACTIONr_scangle_it3.7234.5508
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 57 -
Rwork0.225 968 -
all-1025 -
obs-1025 99.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9514-0.3531-0.67114.65971.49063.39390.058-0.1480.1013-0.01920.0091-0.1487-0.12060.1197-0.0670.075-0.0293-0.00920.02850.00180.010241.448218.918220.5481
23.65850.01360.95293.2780.08163.74020.1078-0.2148-0.28260.13970.10550.03290.15130.0065-0.21330.0323-0.02290.00020.0482-0.00080.036224.988233.358231.3391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 115

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