PDB-4pc4: Bombyx mori lipoprotein 6

ID or keywords:

Entry

Database: PDB / ID: 4pc4

Title

Bombyx mori lipoprotein 6

Components

30K lipoprotein

Keywords

LIPID BINDING PROTEIN / 30-kDa lipoprotein / hemolymph

Function / homology

Function and homology information

extracellular region
Similarity search - Function

Biological species

Bombyx mori (domestic silkworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.8 Å

Authors

Pietrzyk, A.J. / Bujacz, A. / Jaskolski, M. / Bujacz, G.

Citation

Journal: Plos One / Year: 2014
Title: Crystal structure of Bombyx mori lipoprotein 6: comparative structural analysis of the 30-kDa lipoprotein family.
Authors: Pietrzyk, A.J. / Bujacz, A. / ochynska, M. / Jaskolski, M. / Bujacz, G.

History

Deposition	Apr 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release
Revision 2.0	Nov 22, 2017	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy Category: atom_site_anisotrop / diffrn_source ...atom_site_anisotrop / diffrn_source / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.1	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pc4.cif.gz	517.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4pc4.ent.gz	428.9 KB	Display	PDB format
PDBx/mmJSON format	4pc4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pc4_validation.pdf.gz	497.7 KB	Display	wwPDB validaton report
Full document	4pc4_full_validation.pdf.gz	514.7 KB	Display
Data in XML	4pc4_validation.xml.gz	57.5 KB	Display
Data in CIF	4pc4_validation.cif.gz	83.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pc/4pc4 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pc4	HTTPS FTP

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Related structure data

Related structure data	3pub 4efp 4efq 4efr 4iy8 4iy9
Similar structure data	3al3-d 6oa6-d 3ipr-1 4efp-1 2d04-1 1wku-2 5nei-d 1wku-1 5d9z-d 4qhi-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: 30K lipoprotein

B: 30K lipoprotein

C: 30K lipoprotein

D: 30K lipoprotein

E: 30K lipoprotein

hetero molecules

143 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 30K lipoprotein

hetero molecules

defined by author
28.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 30K lipoprotein

hetero molecules

defined by author
28.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 30K lipoprotein

hetero molecules

defined by author
28.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: 30K lipoprotein

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: 30K lipoprotein

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.210, 85.750, 104.470
Angle α, β, γ (deg.)	90.00, 104.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	PHE	PHE	A	A	8 - 245	8 - 245
2	1	ASP	ASP	PHE	PHE	B	B	8 - 245	8 - 245
1	2	ASP	ASP	PRO	PRO	A	A	8 - 244	8 - 244
2	2	ASP	ASP	PRO	PRO	C	C	8 - 244	8 - 244
1	3	ASP	ASP	PHE	PHE	A	A	8 - 245	8 - 245
2	3	ASP	ASP	PHE	PHE	D	D	8 - 245	8 - 245
1	4	ASP	ASP	PRO	PRO	A	A	8 - 244	8 - 244
2	4	ASP	ASP	PRO	PRO	E	E	8 - 244	8 - 244
1	5	ASP	ASP	PRO	PRO	B	B	8 - 244	8 - 244
2	5	ASP	ASP	PRO	PRO	C	C	8 - 244	8 - 244
1	6	ASP	ASP	PHE	PHE	B	B	8 - 245	8 - 245
2	6	ASP	ASP	PHE	PHE	D	D	8 - 245	8 - 245
1	7	ASP	ASP	PRO	PRO	B	B	8 - 244	8 - 244
2	7	ASP	ASP	PRO	PRO	E	E	8 - 244	8 - 244
1	8	ASP	ASP	PRO	PRO	C	C	8 - 244	8 - 244
2	8	ASP	ASP	PRO	PRO	D	D	8 - 244	8 - 244
1	9	ALA	ALA	PRO	PRO	C	C	7 - 244	7 - 244
2	9	ALA	ALA	PRO	PRO	E	E	7 - 244	7 - 244
1	10	ASP	ASP	PRO	PRO	D	D	8 - 244	8 - 244
2	10	ASP	ASP	PRO	PRO	E	E	8 - 244	8 - 244

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	30K lipoprotein Mass: 28313.660 Da / Num. of mol.: 5 / Fragment: UNP residues 17-261 / Source method: isolated from a natural source / Source: (natural) Bombyx mori (domestic silkworm) / Plasmid details: hemolymph / References: UniProt: A7LIK7

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Non-polymers , 5 types, 1144 molecules

#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1131 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.62 Å³/Da / Density % sol: 53.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% isopropanol, 10% PEG 3350, 0.1 M MES

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.05 Å / Num. all: 124752 / Num. obs: 123486 / % possible obs: 94.9 % / Redundancy: 6.44 % / R_merge(I) obs: 0.048 / Net I/σ(I): 22.32
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 3.48 / % possible all: 73

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHASER		phasing
REFMAC	5.7.0032	refinement

Refinement

Resolution: 1.8→47 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.963 / SU B: 4.767 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18264	1265	1 %	RANDOM
R_work	0.16126	-	-	-
obs	0.16147	123486	94.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.053 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3 Å²	0 Å²	-0.36 Å²
2-	-	-0.27 Å²	0 Å²
3-	-	-	0.59 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9779	0	87	1131	10997

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	10215
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	9475
X-RAY DIFFRACTION	r_angle_refined_deg	1.528	1.936	13847
X-RAY DIFFRACTION	r_angle_other_deg	1.489	3.001	21674
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.529	5	1221
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.688	24.183	557
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.679	15	1719
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.991	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	1461
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	11794
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2633
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.858	2.419	4801
X-RAY DIFFRACTION	r_mcbond_other	1.856	2.418	4800
X-RAY DIFFRACTION	r_mcangle_it	2.741	3.616	6000
X-RAY DIFFRACTION	r_mcangle_other	2.741	3.616	6001
X-RAY DIFFRACTION	r_scbond_it	2.641	2.727	5414
X-RAY DIFFRACTION	r_scbond_other	2.637	2.727	5414
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.041	3.976	7831
X-RAY DIFFRACTION	r_long_range_B_refined	7.333	21.347	13034
X-RAY DIFFRACTION	r_long_range_B_other	7.333	21.35	13035
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15095	0.08
1	2	B	15095	0.08
2	1	A	14885	0.09
2	2	C	14885	0.09
3	1	A	15023	0.09
3	2	D	15023	0.09
4	1	A	14951	0.09
4	2	E	14951	0.09
5	1	B	14752	0.1
5	2	C	14752	0.1
6	1	B	14969	0.09
6	2	D	14969	0.09
7	1	B	14703	0.1
7	2	E	14703	0.1
8	1	C	14843	0.1
8	2	D	14843	0.1
9	1	C	14698	0.1
9	2	E	14698	0.1
10	1	D	14700	0.09
10	2	E	14700	0.09

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	66	-
R_work	0.241	6497	-
obs	-	-	68.04 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.3071	-0.3986	0.9384	0.8258	-0.0973	1.0981	-0.0598	-0.2791	-0.0766	0.0473	0.0741	0.0674	0.0724	-0.234	-0.0143	0.0383	-0.0323	0.0059	0.0826	0.0094	0.0066	31.7122	33.3094	85.4401
2	1.4153	-0.3389	0.3818	1.0155	-0.3479	1.048	-0.0429	0.055	-0.0358	-0.0409	-0.0229	-0.1687	0.0638	0.1502	0.0658	0.0288	-0.0056	-0.0031	0.0321	0.0147	0.048	57.1622	31.8849	84.8744
3	1.2359	0.4855	-0.2099	2.0634	-0.4613	1.0184	0.0506	-0.0413	-0.1296	0.0155	-0.082	0.135	0.1119	0.0446	0.0314	0.0394	-0.0174	-0.0027	0.0214	0.0024	0.0357	21.6299	9.9876	67.89
4	0.6379	-0.1911	0.335	1.5589	-0.5825	1.1897	0.0043	-0.0076	0.0522	-0.0752	-0.0194	0.1405	-0.0919	-0.0192	0.0151	0.0469	-0.0183	-0.0201	0.0194	0.0024	0.0243	20.1177	33.0746	57.092
5	0.6364	-0.1734	-0.0778	1.7354	0.3195	0.9142	0.0568	0.0188	-0.0754	-0.1112	-0.0953	-0.0101	-0.0106	-0.0509	0.0385	0.0572	-0.0303	-0.0299	0.044	0.0141	0.0267	45.7967	53.648	66.8452
6	0.9698	0.1089	0.1265	1.2445	0.4434	0.9994	-0.0124	-0.0961	0.1311	-0.029	-0.0832	0.0356	-0.1395	-0.1159	0.0956	0.0683	-0.0196	-0.0302	0.059	-0.0185	0.0378	46.6367	75.6058	80.7096
7	1.4492	0.6628	0.7205	0.9667	0.4992	1.7601	-0.0282	-0.0737	0.0191	-0.0401	-0.0917	0.1733	0.0582	-0.3503	0.1199	0.0666	-0.076	0.0542	0.1534	-0.0546	0.184	-7.5864	5.1326	78.6407
8	1.4029	0.0744	-0.0535	0.7814	0.0008	0.8948	0.0952	-0.3695	0.1471	0.1728	-0.1146	0.0802	0.0129	0.0648	0.0193	0.1183	-0.1071	0.0592	0.1875	-0.0466	0.0672	9.6977	12.348	96.0593
9	2.2005	0.8635	-0.296	1.0519	-0.3572	1.364	-0.007	-0.0552	-0.373	0.0447	0.0823	-0.4172	0.0742	0.1487	-0.0753	0.053	-0.0276	-0.0526	0.0974	-0.023	0.2693	-10.243	60.0007	81.561
10	2.1471	0.653	-1.6428	0.7221	-0.5603	1.8831	-0.2784	0.2643	-0.2754	-0.2272	0.0856	-0.2411	0.1827	-0.0954	0.1928	0.1287	-0.1139	0.14	0.1555	-0.0997	0.2358	4.6484	68.5909	62.3285

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 91
2	X-RAY DIFFRACTION	2	A	92 - 245
3	X-RAY DIFFRACTION	3	B	8 - 91
4	X-RAY DIFFRACTION	4	B	92 - 245
5	X-RAY DIFFRACTION	5	C	6 - 91
6	X-RAY DIFFRACTION	6	C	92 - 245
7	X-RAY DIFFRACTION	7	D	8 - 91
8	X-RAY DIFFRACTION	8	D	92 - 245
9	X-RAY DIFFRACTION	9	E	7 - 91
10	X-RAY DIFFRACTION	10	E	92 - 245

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