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- PDB-3jsa: Homoserine dehydrogenase from Thermoplasma volcanium complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3jsa
TitleHomoserine dehydrogenase from Thermoplasma volcanium complexed with NAD
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / APC89447 / homoserine / dehydrogenase / NAD / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding
Similarity search - Function
Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / homoserine dehydrogenase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsOsipiuk, J. / Nocek, B. / Hendricks, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of Homoserine dehydrogenase from Thermoplasma volcanium
Authors: Osipiuk, J. / Nocek, B. / Hendricks, R. / Abdullah, J. / Joachimiak, A.
History
DepositionSep 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6123
Polymers36,8531
Non-polymers7592
Water3,765209
1
A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2256
Polymers73,7062
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5280 Å2
ΔGint-51 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.043, 110.043, 60.453
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

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Components

#1: Protein Homoserine dehydrogenase /


Mass: 36852.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: GSS1 / Gene: TV0389, TVG0375766 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97BR6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 2 M ammonium sulfate, NAD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 20, 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: 1.95→40.7 Å / Num. all: 30935 / Num. obs: 30935 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.821 / Net I/σ(I): 21.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.42 / Num. unique all: 1536 / Χ2: 0.945 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→40.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.898 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1557 5 %RANDOM
Rwork0.179 ---
all0.181 30873 --
obs0.181 30873 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.97 Å2 / Biso mean: 26.157 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 49 209 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222662
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9963609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48124125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9141520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021990
X-RAY DIFFRACTIONr_mcbond_it0.9661.51604
X-RAY DIFFRACTIONr_mcangle_it1.69222584
X-RAY DIFFRACTIONr_scbond_it2.69431058
X-RAY DIFFRACTIONr_scangle_it4.2274.51018
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 121 -
Rwork0.281 2117 -
all-2238 -
obs-2238 98.9 %
Refinement TLS params.Method: refined / Origin x: -0.9645 Å / Origin y: 81.9321 Å / Origin z: 0.2551 Å
111213212223313233
T0.1292 Å20.001 Å20.0252 Å2-0.0213 Å2-0.0013 Å2--0.064 Å2
L0.595 °20.5679 °20.3806 °2-1.0618 °2-0.196 °2--0.9739 °2
S-0.033 Å °0.0199 Å °-0.0439 Å °-0.0576 Å °0.0035 Å °-0.0026 Å °0.0734 Å °0.0177 Å °0.0295 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 325
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1A329 - 539

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