1k7w

Crystal Structure of S283A Duck Delta 2 Crystallin Mutant

Method: X-RAY DIFFRACTION D_max: 117.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

delta 2 crystallin

Anas platyrhynchos

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–468 Chain B； UniProt 1–468 Chain C； UniProt 1–468 Chain D； UniProt 1–468	Mutation：S283A	AS1 ARGININOSUCCINATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；12% PEG 2000 MME, 300 mM magnesium chloride, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1K7W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUW H91N DELTA 2 CRYSTALLIN FROM DUCK Deposited 1997-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–468（468 aa） Chain B 1–468（468 aa） Chain C 1–468（468 aa） Chain D 1–468（468 aa）	Mutation：H89N Mutation：H89N Mutation：H89N Mutation：H89N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 18-20% PEG MME 2K, 300 MM MGCL2,100 MM TRIS-HCL PH 8.5	Resolution 2.50 Å R-free 0.235
1DCN INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSUCCINATE Deposited 1998-10-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 19–465（447 aa） Chain B 19–465（447 aa） Chain C 19–465（447 aa） Chain D 19–465（447 aa）	Mutation：H162N Mutation：H162N Mutation：H162N Mutation：H162N	AS1 ARGININOSUCCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.30 Å R-free 0.290
1HY1 CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 2 CRYSTALLIN (EYE LENS PROTEIN) Deposited 2001-01-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–468（468 aa） Chain B 1–468（468 aa） Chain C 1–468（468 aa） Chain D 1–468（468 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；14% PEG 2000 MME, 300mM magnesium chloride, 100mM HEPES, pH 7.5. VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 2.30 Å R-free 0.263
1TJU Crystal Structure of T161S Duck Delta 2 Crystallin Mutant Deposited 2004-06-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain B 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain C 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain D 1–468（468 aa） Fragment：Duck delta 2 crystallin	Mutation：T161S Mutation：T161S Mutation：T161S Mutation：T161S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；14% PEG2000 MME, 300 mM magnesium chloride, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.221
1TJV Crystal Structure of T161D Duck Delta 2 Crystallin Mutant Deposited 2004-06-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain B 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain C 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain D 1–468（468 aa） Fragment：Duck delta 2 crystallin	Mutation：T161D Mutation：T161D Mutation：T161D Mutation：T161D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；14% PEG2000 MME, 350 mM magnesium chloride, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.213
1TJW Crystal Structure of T161D Duck Delta 2 Crystallin Mutant with bound argininosuccinate Deposited 2004-06-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain B 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain C 1–468（468 aa） Fragment：Duck delta 2 crystallin Chain D 1–468（468 aa） Fragment：Duck delta 2 crystallin	Mutation：T161D Mutation：T161D Mutation：T161D Mutation：T161D	AS1 ARGININOSUCCINATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；14% PEG2000 MME, 350 mM magnesium chloride, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.225

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CRD2_ANAPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–468； UniProt 1–468 Author chain B； PDBConstruct 1–468； UniProt 1–468 Author chain C； PDBConstruct 1–468； UniProt 1–468 Author chain D； PDBConstruct 1–468； UniProt 1–468

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k7w
Deposition date deposition_date	2001-10-22
Structure title title	Crystal Structure of S283A Duck Delta 2 Crystallin Mutant
Keywords keywords	eye lens protein, delta 2 crystallin, argininosuccinate lyase, enzyme mechanism, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.67 Å
Radius of gyration Rg (electron density) rg_electron	35.97 Å
Forward intensity I(0) i0	569322000.00
Molecular weight molecular_weight	199490.0 kDa
Excluded volume excluded_volume	252270 Å³
Envelope volume envelope_volume	299280 Å³
Hydration-shell volume shell_volume	65893 Å³
Envelope diameter envelope_diameter	129.1 Å
Shell Rg shell_rg	44.56 Å
Envelope Rg envelope_rg	36.35 Å
Shape Rg shape_rg	35.96 Å
Total Rg total_rg	36.51 Å
Total atoms total_atoms	14012
Residues n_residues	1795
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.5 Å
Rg (real space) rg_real	36.49 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	5.6930e+08
I(0) uncertainty (real space) i0_real_error	9.0710e+06
Rg (reciprocal space) rg_reciprocal	36.60 Å
I(0) (reciprocal space) i0_reciprocal	569400000.0000
Solution quality estimate total_estimate	0.8934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	114.8 Å
Skewness Skewness skewness	0.193
Kurtosis Kurtosis kurtosis	-0.456
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	228000000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	delta 2 crystallin
Molecular weight formula_weight	51743.4 kDa
EC 编号 ec_number	4.3.2.1
Mutation mutation	S283A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14719

MASEARGDKLWGGRFSGSTDPIMEKLNSSIAYDQRLSEVDIQGSMAYAKALEKAGILTKTELEKILSGLEKISEEWSKGVFVVKQSDEDIHTANERRLKELIGDIAGKLHTGRSRNDQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSFATLLMIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGASLMPQKKNPDSLELIRSKAGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVFDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGVPFRQAHTASGKAVHLAETKGITINKLSLEDLKSISPQFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKEQA

来源 Source

来源生物 organism	Anas platyrhynchos
NCBI Class编号 ncbi_taxonomy_id	8839
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ARGININOSUCCINATE
Molecular weight formula_weight	290.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	707

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1k7wa_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1k7wb_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1k7wc_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1k7wd_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

CATH v4.4 (12 domains)

Domain ID domain_id	1k7wA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1k7wA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1k7wA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1k7wB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1k7wB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1k7wB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1k7wC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1k7wC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1k7wC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1k7wD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1k7wD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1k7wD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

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8. Citations (1)

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Unit-cell length a length_a	93.759 Å
Unit-cell length b length_b	98.637 Å
Unit-cell length c length_c	106.147 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	19.810 Å
R factor r_factor	0.2240
R_work r_work	0.2070
R_free r_free	0.2530

fit	/app/data/saxs_computation/k7/1k7w/1k7w.fit
pddf	/app/data/pr_computation/k7/1k7w/1k7w.pr.out
profile	/app/data/saxs_computation/k7/1k7w/1k7w.dat