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- PDB-1hy0: CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYE LENS ... -

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Basic information

Entry
Database: PDB / ID: 1hy0
TitleCRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYE LENS PROTEIN)
ComponentsDELTA CRYSTALLIN I
KeywordsLYASE / EYE LENS PROTEIN / DELTA 1 CRYSTALLIN / ARGININOSUCCINATE LYASE
Function / homology
Function and homology information


arginine biosynthetic process via ornithine / structural constituent of eye lens / catalytic activity
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
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSampaleanu, L.M. / Vallee, F. / Slingsby, C. / Howell, P.L.
CitationJournal: Biochemistry / Year: 2001
Title: Structural studies of duck delta 1 and delta 2 crystallin suggest conformational changes occur during catalysis.
Authors: Sampaleanu, L.M. / Vallee, F. / Slingsby, C. / Howell, P.L.
History
DepositionJan 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DELTA CRYSTALLIN I
B: DELTA CRYSTALLIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6144
Polymers102,4222
Non-polymers1922
Water9,296516
1
A: DELTA CRYSTALLIN I
B: DELTA CRYSTALLIN I
hetero molecules

A: DELTA CRYSTALLIN I
B: DELTA CRYSTALLIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,2288
Polymers204,8444
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area31330 Å2
ΔGint-245 kcal/mol
Surface area54910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.6, 100.6, 168.0
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation -x, y-x, 1/3-z

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Components

#1: Protein DELTA CRYSTALLIN I / E.C.4.3.2.1 / DELTA-1-CRYSTALLIN


Mass: 51210.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P24057, argininosuccinate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 550 MME, 10mM zinc sulphate, 100mM MES, pH 6.5. VAPOR DIFFUSION, HANGING DROP at 298 K, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
215 %mPEG5501reservoir
310 mM1reservoirZnSO4
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationMonochromator: parabolic collimating mirror placed upstream of crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 48769 / Num. obs: 48769 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.29 / Num. unique all: 4697 / % possible all: 94.2
Reflection
*PLUS
Num. measured all: 147604
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 576798.15 / 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
Rfree0.233 4749 10.1 %RANDOM
Rwork0.19 ---
all0.207 47139 --
obs0.207 47139 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.34 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-2.53 Å20 Å2
2---1.98 Å20 Å2
3---3.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 10 516 7438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 753 10.3 %
Rwork0.239 6545 -
obs-6545 87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DDC1_FINAL_REN_CIS.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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