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- PDB-1u16: Crystal structure of a duck-delta-crystallin-1 double loop mutant... -

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Basic information

Entry
Database: PDB / ID: 1u16
TitleCrystal structure of a duck-delta-crystallin-1 double loop mutant (DLM) in complex with sulfate
ComponentsDelta crystallin I
KeywordsLYASE / eye lens protein / duck-delta-crystallin / argininosuccinate lyase / enzyme mechanism
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
AuthorsTsai, M. / Sampaleanu, L.M. / Greene, C. / Creagh, L. / Haynes, C. / Howell, P.L.
CitationJournal: Biochemistry / Year: 2004
Title: A duck delta1 crystallin double loop mutant provides insight into residues important for argininosuccinate lyase activity.
Authors: Tsai, M. / Sampaleanu, L.M. / Greene, C. / Creagh, L. / Haynes, C. / Howell, P.L.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6116
Polymers52,2131
Non-polymers3985
Water3,639202
1
A: Delta crystallin I
hetero molecules

A: Delta crystallin I
hetero molecules

A: Delta crystallin I
hetero molecules

A: Delta crystallin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,44224
Polymers208,8524
Non-polymers1,59120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area33820 Å2
ΔGint-313 kcal/mol
Surface area56330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.280, 133.280, 73.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2283-

HOH

Detailsbiological assembly is a homotetramer

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Components

#1: Protein Delta crystallin I


Mass: 52212.926 Da / Num. of mol.: 1
Mutation: Q22E,M23K,S25N,T26S,S29A,T30Y,E31D,L74W,I79F,T82K,Q89H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / References: UniProt: P24057, argininosuccinate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.28 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, cobalt chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.2→58.16 Å / Num. obs: 34371 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 12.9 Å2 / Limit h max: 60 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 746250.89 / Observed criterion F min: 5.166 / Rsym value: 0.087
Reflection shellResolution: 2.2→2.28 Å / Rsym value: 0.32 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code:1HY1

1hy1


Resolution: 2.2→58.16 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3420 10 %random
Rwork0.212 ---
obs-34287 99.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 62.3048 Å2 / ksol: 0.371665 e/Å3
Displacement parametersBiso max: 106.08 Å2 / Biso mean: 38.61 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1--16.81 Å20 Å20 Å2
2---16.81 Å20 Å2
3---33.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.44 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→58.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 20 202 3700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg19.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.30.39545210.80.38337500.0194238420299.1
2.3-2.420.3543810.40.30337780.0174227421699.7
2.42-2.570.3133999.50.25638200.01642194219100
2.57-2.770.2774079.50.22938610.0144278426899.8
2.77-3.050.3174129.70.23938370.01642504249100
3.05-3.490.27644610.40.22438450.0134301429199.8
3.49-4.40.2214239.80.16238990.0114333432299.7
4.4-58.160.2044439.80.16540770.014560452099.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4mes_param.cns
X-RAY DIFFRACTION5ion.param

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