SAXSdb — 1cd3

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1. Structure Basics

entry_id	1cd3
deposition_date	1999-03-05
title	PROCAPSID OF BACTERIOPHAGE PHIX174
keywords	COMPLEX (VIRUS CAPSID PROTEINS), BACTERIOPHAGE, PROCAPSID, SCAFFOLDING PROTEIN, CHAPERONE, Icosahedral virus, Virus; VIRUS
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	35.98 Å
rg_electron	35.09 Å
i0	292532000.00
molecular_weight	138320.0 kDa
excluded_volume	173230 Å³
envelope_volume	235970 Å³
shell_volume	54525 Å³
envelope_diameter	116.5 Å
shell_rg	42.59 Å
envelope_rg	35.10 Å
shape_rg	35.06 Å
total_rg	35.73 Å
total_atoms	9755
n_residues	1233
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	108.8 Å
rg_real	35.76 Å
rg_real_error	0.53 Å
i0_real	2.9250e+08
i0_real_error	4.1890e+06
rg_reciprocal	35.90 Å
i0_reciprocal	292600000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	47.0 Å
skewness	0.078
kurtosis	-0.570
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	46470000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTEIN (SCAFFOLDING PROTEIN GPD)
formula_weight	16953.3 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	1,2,3,4
atom_count	9851

MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM

Entity 2 polymer

description	PROTEIN (CAPSID PROTEIN GPF)
formula_weight	48407.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARFGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS

Entity 3 polymer

description	PROTEIN (SPIKE PROTEIN GPG)
formula_weight	19061.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK

Entity 4 polymer

description	PROTEIN (SCAFFOLDING PROTEIN GPB)
formula_weight	13863.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTYQAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (7)

The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.

J.Mol.Biol. (1999)

PMID: 10329166 · DOI: 10.1006/jmbi.1999.2699 PRIMARY

Structure of a viral procapsid with molecular scaffolding.

Nature (1997)

PMID: 9305849 · DOI: 10.1038/38537

DNA packaging intermediates of bacteriophage phi X174.

Structure (1995)

PMID: 7613866 · DOI: 10.1016/s0969-2126(01)00167-8

Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.

J.Mol.Biol. (1994)

PMID: 8158636 · DOI: 10.1006/jmbi.1994.1253

Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications.

Nature (1992)

PMID: 1370343 · DOI: 10.1038/355137a0

The Bacteriophages

The Bacteriophages (The Viruses) (1988)

Nucleotide sequence of bacteriophage phi X174 DNA.

Nature (1977)

PMID: 870828 · DOI: 10.1038/265687a0

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length_a	774.000 Å
length_b	774.000 Å
length_c	774.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	96

space_group	I 21 3
int_tables_number	199
crystal_system	—

resolution	3.500 Å
resolution_low	8.000 Å
r_factor	—
r_work	0.2750
r_free	—

fit	/app/data/saxs_computation/cd/1cd3/1cd3.fit
pddf	/app/data/pr_computation/cd/1cd3/1cd3.pr.out
profile	/app/data/saxs_computation/cd/1cd3/1cd3.dat

PROCAPSID OF BACTERIOPHAGE PHIX174

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

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 water

6. Citations (7)

7. Files & Curves (10)

Files (7)

Curves (3)