SAXSdb — 1cf8

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN)) × 1 Entity 2：PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN)) × 1 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：FAB, VARIABLE REGION Entity 2Fragment：FAB, VARIABLE REGION	CD CADMIUM ION × 2 HAZ 4-{4-[2-(1A,7A-DIMETHYL-4-OXY-OCTAHYDRO-1-OXA-4-AZA-CYCLOPROPA[A]NAPHTHALEN-4-YL) -ACETYLAMINO]-PHENYLCARBAMOYL}-BUTYRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；DROP: 11.4 MG/ML FAB, 10MM CDCL2, 50 MM TRIS, PH 7.0, RESERVOIR: 30% PEG 6000, 100 MM HEPES PH 7.9, pH 7.00	Resolution 2.70 Å R-free 0.257
2	Protein heterocomplex Heteromer 蛋白 4 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: tetrameric	Entity 1：PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN)) × 2 Entity 2：PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN)) × 2 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：FAB, VARIABLE REGION Entity 2Fragment：FAB, VARIABLE REGION	CD CADMIUM ION × 4 HAZ 4-{4-[2-(1A,7A-DIMETHYL-4-OXY-OCTAHYDRO-1-OXA-4-AZA-CYCLOPROPA[A]NAPHTHALEN-4-YL) -ACETYLAMINO]-PHENYLCARBAMOYL}-BUTYRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；DROP: 11.4 MG/ML FAB, 10MM CDCL2, 50 MM TRIS, PH 7.0, RESERVOIR: 30% PEG 6000, 100 MM HEPES PH 7.9, pH 7.00	Resolution 2.70 Å R-free 0.257

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cf8
Deposition date deposition_date	1999-03-24
Structure title title	Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by carbocation-pi interactions
Keywords keywords	CATALYTIC ANTIBODY, TERPENOID SYNTHASE, CARBOCATION, CYCLIZATION CASCADE; CATALYTIC ANTIBODY
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	25.60 Å
Radius of gyration Rg (electron density) rg_electron	24.51 Å
Forward intensity I(0) i0	39490600.00
Molecular weight molecular_weight	47633.0 kDa
Excluded volume excluded_volume	59002 Å³
Envelope volume envelope_volume	72250 Å³
Hydration-shell volume shell_volume	24722 Å³
Envelope diameter envelope_diameter	79.8 Å
Shell Rg shell_rg	31.57 Å
Envelope Rg envelope_rg	24.16 Å
Shape Rg shape_rg	24.47 Å
Total Rg total_rg	25.41 Å
Total atoms total_atoms	3337
Residues n_residues	433
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	78.2 Å
Rg (real space) rg_real	25.58 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.9490e+07
I(0) uncertainty (real space) i0_real_error	5.8730e+05
Rg (reciprocal space) rg_reciprocal	25.59 Å
I(0) (reciprocal space) i0_reciprocal	39490000.0000
Solution quality estimate total_estimate	0.9096
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6554000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.897

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))
Molecular weight formula_weight	23484.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3348

DIVLTQSPTIMSVSPGEKVTLTCSASSSVSSNYVYWYQQKPGSSPKVWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAASYFCLQWSSFPYTFGGGTKLELKRADVAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))
Molecular weight formula_weight	23500.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DVQLQESGPGLVKPSQSLSLTCTVTGYSITSGYAWNWIRQFPGNKLEWMGYIRYSGDTRYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAIGYGNSDYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHAFPALLQSDLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPKDC

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	4-{4-[2-(1A,7A-DIMETHYL-4-OXY-OCTAHYDRO-1-OXA-4-AZA-CYCLOPROPA[A]NAPHTHALEN-4-YL) -ACETYLAMINO]-PHENYLCARBAMOYL}-BUTYRIC ACID
Molecular weight formula_weight	459.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cf8h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1cf8h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1cf8l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1cf8l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1cf8H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cf8H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cf8L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cf8L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	101.300 Å
Unit-cell length b length_b	70.300 Å
Unit-cell length c length_c	69.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1650
R_free r_free	0.2570

fit	/app/data/saxs_computation/cf/1cf8/1cf8.fit
pddf	/app/data/pr_computation/cf/1cf8/1cf8.pr.out
profile	/app/data/saxs_computation/cf/1cf8/1cf8.dat

Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by carbocation-pi interactions

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

Assembly Composition of the Current Entry

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)