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1d6v

CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION

Method: X-RAY DIFFRACTION D_max: 82.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d6v
deposition_date	1999-10-15
title	CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION
keywords	IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	25.63 Å
rg_electron	24.76 Å
i0	39431200.00
molecular_weight	47914.0 kDa
excluded_volume	59419 Å³
envelope_volume	73675 Å³
shell_volume	25043 Å³
envelope_diameter	84.5 Å
shell_rg	31.86 Å
envelope_rg	24.45 Å
shape_rg	24.77 Å
total_rg	25.53 Å
total_atoms	3348
n_residues	432
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	82.7 Å
rg_real	25.60 Å
rg_real_error	0.53 Å
i0_real	3.9430e+07
i0_real_error	5.1850e+05
rg_reciprocal	25.61 Å
i0_reciprocal	39430000.0000
total_estimate	0.9062
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.261
kurtosis	-0.529
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	5537000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN)
formula_weight	23506.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	3486

DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN)
formula_weight	23618.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGHSYYFYDGDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	CADMIUM ION
formula_weight	112.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL
formula_weight	381.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	138

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6. Citations (1)

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length_a	52.718 Å
length_b	64.446 Å
length_c	73.870 Å
angle_alpha	90.00 °
angle_beta	99.09 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	9.920 Å
r_factor	0.2240
r_work	0.2240
r_free	0.2640

fit	/app/data/saxs_computation/d6/1d6v/1d6v.fit
pddf	/app/data/pr_computation/d6/1d6v/1d6v.pr.out
profile	/app/data/saxs_computation/d6/1d6v/1d6v.dat

CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)