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- PDB-1auw: H91N DELTA 2 CRYSTALLIN FROM DUCK -

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Basic information

Entry
Database: PDB / ID: 1auw
TitleH91N DELTA 2 CRYSTALLIN FROM DUCK
ComponentsDELTA 2 CRYSTALLIN
KeywordsEYE LENS PROTEIN / DELTA 2 CRYSTALLIN / ARGINOSUCCINATE 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 lyase
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAbu-Abed, M. / Vallee, F. / Howell, P.L.
CitationJournal: Biochemistry / Year: 1997
Title: Structural comparison of the enzymatically active and inactive forms of delta crystallin and the role of histidine 91.
Authors: Abu-Abed, M. / Turner, M.A. / Vallee, F. / Simpson, A. / Slingsby, C. / Howell, P.L.
History
DepositionSep 3, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: 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 / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)206,9494
Polymers206,9494
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29060 Å2
ΔGint-159 kcal/mol
Surface area57880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 100.200, 109.100
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.62853, 0.05304, 0.77598), (0.04926, -0.99295, 0.10777), (0.77623, 0.10596, 0.62149)12.68913, -5.87184, -5.64835
2given(0.04056, -0.89661, -0.44095), (-0.8993, -0.22509, 0.37496), (-0.43544, 0.38134, -0.81546)33.12549, 7.31229, 63.52295
3given(-0.41755, 0.84367, -0.33746), (0.84257, 0.22044, -0.49141), (-0.34019, -0.48952, -0.80289)41.5766, -4.51147, 60.15944

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Components

#1: Protein
DELTA 2 CRYSTALLIN


Mass: 51737.242 Da / Num. of mol.: 4 / Mutation: H89N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Cell line: BL21 / Organ: EYE / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P24058, argininosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 9

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18-20% PEG MME 2K, 300 MM MGCL2,100 MM TRIS-HCL PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-8 mg/mlprotein1drop
250 mMTris-HCl1drop
39-10 %(w/v)PEG MME20001drop
4150 mM1dropMgCl2
550 mMTris-HCl1drop
618-20 %(w/v)PEG MME20001reservoir
7300 mM1reservoirMgCl2
8100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 65641 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.103
Reflection shellResolution: 2.5→2.6 Å / Rsym value: 0.33 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 239855 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TURKEY DELTA 1 CRYSTALLINE

Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: CIS PEPTIDES NOT INCLUDED IN DIHEDRAL ANGLES. X-PLOR 3.1 ALSO WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 -10 %RANDOM
Rwork0.161 ---
obs0.161 57985 93 %-
Displacement parametersBiso mean: 31.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13912 0 0 343 14255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.86
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.86

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