PDB-8i34: The crystal structure of EPD-BCP1 from a marine sponge

ID or keywords:

Entry

Database: PDB / ID: 8i34

Title

The crystal structure of EPD-BCP1 from a marine sponge

Components

alpha subunit of EPD-BCP1
beta subunit of EPD-BCP1

Keywords

LIPID BINDING PROTEIN / ependymin family / carotenoprotein / astaxanthin / mytiloxanthin / coloration / bathochromic shift / N-glycosylation / marine blue sponge

Function / homology

ASTAXANTHIN / Chem-O1U

Function and homology information

Biological species

Haliclona sp. (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Shomura, Y. / Kawasaki, S.

Funding support

Japan, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: An ependymin-related blue carotenoprotein decorates marine blue sponge.
Authors: Kawasaki, S. / Kaneko, T. / Asano, T. / Maoka, T. / Takaichi, S. / Shomura, Y.

History

Deposition	Jan 16, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8i34.cif.gz	307.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8i34.ent.gz	242.4 KB	Display	PDB format
PDBx/mmJSON format	8i34.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8i34_validation.pdf.gz	4.8 MB	Display	wwPDB validaton report
Full document	8i34_full_validation.pdf.gz	4.8 MB	Display
Data in XML	8i34_validation.xml.gz	54.8 KB	Display
Data in CIF	8i34_validation.cif.gz	74.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/8i34 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/8i34	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: alpha subunit of EPD-BCP1

B: beta subunit of EPD-BCP1

C: alpha subunit of EPD-BCP1

D: beta subunit of EPD-BCP1

E: alpha subunit of EPD-BCP1

F: beta subunit of EPD-BCP1

G: alpha subunit of EPD-BCP1

H: beta subunit of EPD-BCP1

hetero molecules

179 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: alpha subunit of EPD-BCP1

B: beta subunit of EPD-BCP1

hetero molecules

defined by author&software
Evidence: gel filtration
44.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: alpha subunit of EPD-BCP1

D: beta subunit of EPD-BCP1

hetero molecules

defined by author&software
44.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: alpha subunit of EPD-BCP1

F: beta subunit of EPD-BCP1

hetero molecules

defined by author&software
44.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: alpha subunit of EPD-BCP1

H: beta subunit of EPD-BCP1

hetero molecules

defined by author&software
44.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.749, 101.380, 112.588
Angle α, β, γ (deg.)	90.000, 95.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	alpha subunit of EPD-BCP1 Mass: 21130.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Haliclona sp. (invertebrata)
#2: Protein	beta subunit of EPD-BCP1 Mass: 21171.057 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Haliclona sp. (invertebrata)

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Sugars , 1 types, 12 molecules

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

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Non-polymers , 3 types, 268 molecules

#4: Chemical	ChemComp-O1U / (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-4,8,13,17-tetramethyl-3-oxidanyl-19-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-1-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-2,4,6,8,10,12,14,16-octaen-18-yn-1-one / mytiloxanthin Mass: 598.854 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄₀H₅₄O₄
#5: Chemical	ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE Mass: 596.838 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄₀H₅₂O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.48 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 2-Amino-2-(hydroxymethyl)propane-1,3-diol, magnesium chloride, polyethylene glycol 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.44→75.32 Å / Num. obs: 61509 / % possible obs: 99.9 % / Redundancy: 3.3 % / B_iso Wilson estimate: 36.8 Å² / CC_1/2: 0.981 / R_merge(I) obs: 0.104 / R_pim(I) all: 0.068 / R_rim(I) all: 0.125 / Net I/σ(I): 7
Reflection shell	Resolution: 2.44→2.5 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.584 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4535 / CC_1/2: 0.746 / R_pim(I) all: 0.385 / R_rim(I) all: 0.702 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
iMOSFLM		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.44→75.32 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.914 / SU B: 11.094 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 0.49 / ESU R Free: 0.274
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2482	2954	4.804 %
R_work	0.2015	58532	-
all	0.204	-	-
obs	-	61486	99.891 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 43.642 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.431 Å²	0 Å²	1.587 Å²
2-	-	-2.54 Å²	-0 Å²
3-	-	-	-2.138 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→75.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10660	0	687	260	11607

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	11623
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	10460
X-RAY DIFFRACTION	r_angle_refined_deg	1.403	1.651	15906
X-RAY DIFFRACTION	r_angle_other_deg	0.489	1.557	24472
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.986	5	1392
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.992	5	208
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.773	10	1724
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.711	10	444
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1840
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	13212
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2172
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1534
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	9164
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	5553
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	6179
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.306	0.2	264
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.066	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	4.311	4.453	5592
X-RAY DIFFRACTION	r_mcbond_other	4.309	4.453	5592
X-RAY DIFFRACTION	r_mcangle_it	6.636	6.67	6976
X-RAY DIFFRACTION	r_mcangle_other	6.636	6.671	6977
X-RAY DIFFRACTION	r_scbond_it	4.348	4.709	6031
X-RAY DIFFRACTION	r_scbond_other	4.347	4.708	6032
X-RAY DIFFRACTION	r_scangle_it	6.654	6.943	8930
X-RAY DIFFRACTION	r_scangle_other	6.653	6.942	8931
X-RAY DIFFRACTION	r_lrange_it	8.97	54.441	11492
X-RAY DIFFRACTION	r_lrange_other	8.97	54.443	11486
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.033	0.05	5212
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.036	0.05	5180
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.036	0.05	5187
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.029	0.05	5203
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.042	0.05	5159
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.039	0.05	5154
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.042	0.05	5196
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.04	0.05	5208
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.035	0.05	5193
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.031	0.05	5184
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.022	0.05	5237
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.035	0.05	5184

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0331	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0331	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.03649	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.03649	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.03564	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.03564	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.02853	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.02853	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04221	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.04221	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.03875	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.03875	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.04158	0.05011
7	14	A	X-RAY DIFFRACTION	Local ncs	0.04158	0.05011
8	15	A	X-RAY DIFFRACTION	Local ncs	0.04032	0.05011
8	16	A	X-RAY DIFFRACTION	Local ncs	0.04032	0.05011
9	17	A	X-RAY DIFFRACTION	Local ncs	0.03545	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.03545	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.03101	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.03101	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.02211	0.05011
11	22	A	X-RAY DIFFRACTION	Local ncs	0.02211	0.05011
12	23	A	X-RAY DIFFRACTION	Local ncs	0.03538	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.03538	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.44-2.503	0.335	216	0.312	4308	0.313	4538	0.907	0.924	99.6915	0.294
2.503-2.572	0.341	215	0.28	4197	0.283	4419	0.921	0.942	99.8416	0.261
2.572-2.646	0.32	195	0.281	4082	0.283	4283	0.926	0.943	99.8599	0.264
2.646-2.728	0.299	199	0.265	3998	0.267	4198	0.935	0.952	99.9762	0.246
2.728-2.817	0.325	172	0.248	3838	0.251	4015	0.931	0.957	99.8755	0.229
2.817-2.916	0.322	189	0.23	3722	0.234	3921	0.94	0.963	99.745	0.212
2.916-3.026	0.314	168	0.227	3577	0.231	3746	0.939	0.965	99.9733	0.212
3.026-3.149	0.273	156	0.217	3501	0.22	3657	0.949	0.969	100	0.206
3.149-3.289	0.257	175	0.204	3321	0.207	3497	0.954	0.973	99.9714	0.196
3.289-3.449	0.251	162	0.211	3152	0.213	3317	0.962	0.972	99.9096	0.205
3.449-3.635	0.249	150	0.203	3045	0.205	3198	0.957	0.975	99.9062	0.201
3.635-3.855	0.247	178	0.196	2819	0.199	2998	0.96	0.977	99.9666	0.197
3.855-4.12	0.236	148	0.179	2699	0.182	2848	0.968	0.98	99.9649	0.183
4.12-4.449	0.172	118	0.153	2508	0.154	2628	0.983	0.986	99.9239	0.161
4.449-4.872	0.17	110	0.129	2312	0.131	2424	0.985	0.99	99.9175	0.142
4.872-5.445	0.17	93	0.142	2103	0.143	2196	0.985	0.989	100	0.152
5.445-6.281	0.213	109	0.17	1855	0.172	1967	0.973	0.983	99.8475	0.179
6.281-7.68	0.234	98	0.19	1552	0.193	1652	0.96	0.977	99.8789	0.2
7.68-10.805	0.239	70	0.181	1231	0.184	1304	0.964	0.978	99.7699	0.196
10.805-75.32	0.293	33	0.286	712	0.286	746	0.931	0.937	99.866	0.317

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