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- PDB-1dcn: INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSU... -

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Basic information

Entry
Database: PDB / ID: 1dcn
TitleINACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSUCCINATE
ComponentsDELTA 2 CRYSTALLIN
KeywordsEYE LENS PROTEIN / DELTA 2 CRYSTALLIN / ARGININOSUCCINATE LYASE
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / L-arginine biosynthetic process via ornithine / structural constituent of eye lens / L-arginine biosynthetic process / cytosol
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 / Fumarase/aspartase (N-terminal domain) ...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 / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVallee, F. / Turner, M.A. / Lindley, P. / Howell, P.L.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate.
Authors: Vallee, F. / Turner, M.A. / Lindley, P.L. / Howell, P.L.
History
DepositionOct 29, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 2, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_stereo_config ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_stereo_config / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA 2 CRYSTALLIN
B: DELTA 2 CRYSTALLIN
C: DELTA 2 CRYSTALLIN
D: DELTA 2 CRYSTALLIN
D: ARGININOSUCCINATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,2935
Polymers198,0034
Non-polymers2901
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24640 Å2
ΔGint-126 kcal/mol
Surface area59210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.580, 99.590, 107.140
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.061, -0.891, -0.45), (-0.9, -0.244, 0.362), (-0.432, 0.383, -0.816)137.459, 87.739, 153.089
2given(-0.616, 0.07, 0.785), (0.053, -0.99, 0.13), (0.786, 0.122, 0.606)27.77, 88.76, -20.515
3given(-0.433, 0.836, -0.338), (0.836, 0.231, -0.498), (-0.338, -0.498, -0.799)68.714, 30.696, 191.461

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Components

#1: Protein
DELTA 2 CRYSTALLIN / DDC2


Mass: 49500.797 Da / Num. of mol.: 4 / Mutation: H162N
Source method: isolated from a genetically manipulated source
Details: ARGININOSUCCINATE BOUND TO ONE ACTIVE SITE / Source: (gene. exp.) Anas platyrhynchos (mallard) / Cell line: 293 / Organ: EYE / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P24058, argininosuccinate lyase
#2: Chemical ChemComp-AS1 / ARGININOSUCCINATE


Mass: 290.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N4O6 / Details: ARGININOSUCCINATE BOUND TO ONE ACTIVE SITE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O / Details: ARGININOSUCCINATE BOUND TO ONE ACTIVE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlenzyme solution1drop
2100 mMTris-HCl1drop
318 %(w/v)PEG MME20001reservoir
4200 mM1reservoirMgCl2
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 77291 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.079
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.233
Reflection
*PLUS
Num. measured all: 194258 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96.4 %

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Processing

Software
NameVersionClassification
AMoRE5.3phasing
CNS0.3Crefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUW

1auw


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 9791538.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 7210 10.1 %RANDOM
Rwork0.229 ---
obs0.229 71225 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.84 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-6.25 Å2
2---5.14 Å20 Å2
3---4.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13263 0 20 471 13754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.13
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 1072 10.4 %
Rwork0.279 9249 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3AS.PARAS.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Lowest resolution: 17 Å / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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