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- PDB-1tjw: Crystal Structure of T161D Duck Delta 2 Crystallin Mutant with bo... -

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Basic information

Entry
Database: PDB / ID: 1tjw
TitleCrystal Structure of T161D Duck Delta 2 Crystallin Mutant with bound argininosuccinate
ComponentsDelta crystallin II
KeywordsLYASE / eye lens protein / delta 2 crystallin / argininosuccinate lyase / enzyme mechanism
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / structural constituent of eye lens / arginine biosynthetic process
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ARGININOSUCCINATE / Argininosuccinate lyase
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSampaleanu, L.M. / Codding, P.W. / Lobsanov, Y.D. / Tsai, M. / Smith, G.D. / Horvatin, C. / Howell, P.L.
CitationJournal: Biochem.J. / Year: 2004
Title: Structural studies of duck delta2 crystallin mutants provide insight into the role of Thr161 and the 280s loop in catalysis
Authors: Sampaleanu, L.M. / Codding, P.W. / Lobsanov, Y.D. / Tsai, M. / Smith, G.D. / Horvatin, C. / Howell, P.L.
History
DepositionJun 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta crystallin II
B: Delta crystallin II
C: Delta crystallin II
D: Delta crystallin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,6268
Polymers210,4654
Non-polymers1,1614
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30940 Å2
ΔGint-127 kcal/mol
Surface area57570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.996, 98.806, 106.387
Angle α, β, γ (deg.)90.00, 101.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the homotetramer with four bound argininosuccinate molecules, as present in the assymetric unit

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Components

#1: Protein
Delta crystallin II / Argininosuccinate lyase


Mass: 52616.234 Da / Num. of mol.: 4 / Fragment: Duck delta 2 crystallin / Mutation: T161D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid / References: UniProt: P24058, argininosuccinate lyase
#2: Chemical
ChemComp-AS1 / ARGININOSUCCINATE / Argininosuccinic acid


Mass: 290.273 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.49 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG2000 MME, 350 mM magnesium chloride, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001
RadiationMonochromator: parabolic collimating mirror placed upstream of the monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→41.8 Å / Num. all: 141060 / Num. obs: 128293 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.063
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HY1

1hy1


Resolution: 2→41.76 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 256303.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 12767 10 %RANDOM
Rwork0.19 ---
all0.2 141060 --
obs0.19 128293 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7916 Å2 / ksol: 0.356132 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å2-2.31 Å2
2---3.76 Å20 Å2
3---6.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13830 0 80 910 14820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 2054 9.7 %
Rwork0.209 19212 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CIS_PEPT161D_AS.PARAMAS.PWC.TOP
X-RAY DIFFRACTION4AS.PWC.PARAM

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