SAXSdb — 9wfc

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1. Structure Basics

entry_id	9wfc
deposition_date	2025-08-21
title	Cryo-EM structure of GGCX-MGP complex
keywords	Vitamin K-dependent gamma-carboxylase binding to its substrate MGP, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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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	29.41 Å
rg_electron	28.58 Å
i0	189601000.00
molecular_weight	76066.0 kDa
excluded_volume	75177 Å³
envelope_volume	130350 Å³
shell_volume	37825 Å³
envelope_diameter	95.9 Å
shell_rg	36.14 Å
envelope_rg	28.64 Å
shape_rg	28.56 Å
total_rg	29.16 Å
total_atoms	5790
n_residues	681
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	94.0 Å
rg_real	29.39 Å
rg_real_error	0.86 Å
i0_real	1.8960e+08
i0_real_error	2.8710e+06
rg_reciprocal	29.40 Å
i0_reciprocal	189600000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.6 Å
skewness	0.329
kurtosis	-0.349
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	22390000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Vitamin K-dependent gamma-carboxylase
formula_weight	81275.9 kDa
ec_number	4.1.1.90
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5790

SRIGKLLGFEWTDLSSWRRLVTLLNRPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRTGELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQRIFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHLENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYMYVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFLRRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEVTYANLRPF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Matrix Gla protein
formula_weight	3336.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

LCYESHESMSYELNPFINRRNANTFISP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	;(2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate ;
formula_weight	701.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	;(1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione ;
formula_weight	460.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.330 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.33 Å
resolution_method	—
num_particles	138030

fit	/app/data/saxs_computation/wf/9wfc/9wfc.fit
pddf	/app/data/pr_computation/wf/9wfc/9wfc.pr.out
profile	/app/data/saxs_computation/wf/9wfc/9wfc.dat

Cryo-EM structure of GGCX-MGP complex

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)