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- PDB-1k7w: Crystal Structure of S283A Duck Delta 2 Crystallin Mutant -

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Basic information

Entry
Database: PDB / ID: 1k7w
TitleCrystal Structure of S283A Duck Delta 2 Crystallin Mutant
Componentsdelta 2 crystallin
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 / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSampaleanu, L.M. / Yu, B. / Howell, P.L.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase.
Authors: Sampaleanu, L.M. / Yu, B. / Howell, P.L.
History
DepositionOct 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 16, 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 2 crystallin
B: delta 2 crystallin
C: delta 2 crystallin
D: delta 2 crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,1358
Polymers206,9734
Non-polymers1,1614
Water12,737707
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30860 Å2
ΔGint-132 kcal/mol
Surface area58130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.759, 98.637, 106.147
Angle α, β, γ (deg.)90.00, 101.30, 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 asymmetric unit

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Components

#1: Protein
delta 2 crystallin


Mass: 51743.355 Da / Num. of mol.: 4 / Mutation: S283A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / 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.: 707 / 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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 2000 MME, 300 mM magnesium chloride, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
31 mMEDTA1drop
475 mMargininosuccinate1drop
512 %(w/v)PEG2000MME1reservoir
6300 mM1reservoirMgCl2
7100 mMHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.96 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2000
RadiationMonochromator: parabolic collimating mirror placed upstream of crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.96→20 Å / Num. all: 125073 / Num. obs: 125073 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 1.96→2.03 Å / Rsym value: 0.34 / % possible all: 91.8
Reflection
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 20 Å / Num. obs: 127416 / % possible obs: 94 % / Num. measured all: 692205 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 91.8 % / Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HY1

1hy1


Resolution: 1.96→19.81 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 299780.83 / 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
Rfree0.253 12440 9.9 %RANDOM
Rwork0.207 ---
all0.224 125073 --
obs0.224 125073 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.7155 Å2 / ksol: 0.393911 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-6.63 Å2
2---1.57 Å20 Å2
3---5.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.96→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13932 0 80 707 14719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 1951 9.9 %
Rwork0.257 17685 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CIS_PEPT.PARAM
X-RAY DIFFRACTION4AS_PAR.TXTAS_TOP.TXT
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Lowest resolution: 2.03 Å / Rfactor Rfree: 0.301 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.257

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