PDB-4efr: Bombyx mori lipoprotein 7 (crystal form II) at 2.50 A resolution

ID or keywords:

Entry

Database: PDB / ID: 4efr

Title

Bombyx mori lipoprotein 7 (crystal form II) at 2.50 A resolution

Components

30kDa protein

Keywords

UNKNOWN FUNCTION /

VHS domain / beta-trefoil domain

Function / homology

Function and homology information

extracellular region
Similarity search - Function

Biological species

Bombyx mori (domestic silkworm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Pietrzyk, A.J. / Panjikar, S. / Bujacz, A. / Mueller-Dieckmann, J. / Jaskolski, M. / Bujacz, G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification.
Authors: Pietrzyk, A.J. / Panjikar, S. / Bujacz, A. / Mueller-Dieckmann, J. / Lochynska, M. / Jaskolski, M. / Bujacz, G.

History

Deposition	Mar 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4efr.cif.gz	386 KB	Display	PDBx/mmCIF format
PDB format	pdb4efr.ent.gz	320.9 KB	Display	PDB format
PDBx/mmJSON format	4efr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/4efr ftp://data.pdbj.org/pub/pdb/validation_reports/ef/4efr	HTTPS FTP

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Related structure data

Related structure data	4efpSC 4efqC 3pub S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4irv-2 4efp-2 4h5x-2 4lkl-d 6ax4-d 4x9r-d 4h5x-1 2hsz-1 4o6w-d 4wda-d 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

4efpSC

4efqC

3pub

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: 30kDa protein

B: 30kDa protein

C: 30kDa protein

D: 30kDa protein

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 30kDa protein

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

2

B: 30kDa protein

hetero molecules

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

3

C: 30kDa protein

hetero molecules

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

4

D: 30kDa protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	35.100, 71.720, 105.120
Angle α, β, γ (deg.)	78.79, 89.98, 75.79
Int Tables number	1
Space group name H-M	P1

#1: Protein	30kDa protein Mass: 27579.088 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: E5EVW2
#2: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES buffer, 22 % PEG 3350, 200 mM KSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.949 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2011
Radiation	Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.949 Å / Relative weight: 1
Reflection	Resolution: 2.5→37 Å / Num. all: 29885 / Num. obs: 29884 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / R_merge(I) obs: 0.043 / Net I/σ(I): 13.88
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.147 / Mean I/σ(I) obs: 4.67 / % possible all: 88.8

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Processing

Software

Name	Version	Classification
XDS		data scaling
Auto-Rickshaw	MR protocol	phasing
REFMAC	5.5.0109	refinement
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4EFP

4efp

Resolution: 2.5→37 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.86 / SU B: 8.329 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28532	949	3.2 %	RANDOM
R_work	0.20112	-	-	-
obs	0.2038	28935	88.82 %	-
all	-	29885	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 36.656 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.42 Å²	0.61 Å²	-0.25 Å²
2-	-	-2.42 Å²	0.87 Å²
3-	-	-	0.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7667	0	12	137	7816

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	7903
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.983	1.949	10689
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.391	5	949
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.889	24.442	403
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.136	15	1375
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.956	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	1119
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6068
X-RAY DIFFRACTION	r_gen_planes_other
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	0.878	1.5	4685
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.468	2	7523
X-RAY DIFFRACTION	r_scbond_it	2.734	3	3218
X-RAY DIFFRACTION	r_scangle_it	3.847	4.5	3159
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	80	-
R_work	0.075	2132	-
obs	-	-	88.73 %

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	6.6104	2.6335	1.3959	1.4478	1.6647	4.05	-0.0261	-0.2107	0.5366	0.0822	-0.096	0.2571	-0.2621	0.1336	0.1221	0.4064	-0.0766	0.0508	0.1074	-0.0163	0.1011	-9.1221	39.222	22.7105
2	2.0451	-1.3119	0.2714	8.046	2.8534	2.0348	-0.1391	-0.0613	0.176	0.0821	0.1687	-0.2425	-0.2196	0.1033	-0.0297	0.0809	-0.0633	-0.0136	0.163	-0.002	0.062	-3.5549	37.2354	17.3029
3	0.3314	-0.9179	-0.3619	3.3188	0.6962	1.3659	0.0042	0.0055	0.0238	-0.2289	-0.0027	0.0181	0.1039	-0.0266	-0.0015	0.0884	-0.0335	-0.0172	0.0324	0.0121	0.1325	-3.0647	18.9074	4.1976
4	1.0078	-0.8991	0.087	1.3412	0.2184	1.2308	-0.002	-0.1186	-0.0352	0.0581	0.0715	-0.1097	0.1413	-0.036	-0.0695	0.0232	-0.008	-0.0089	0.0428	0.0519	0.1754	1.8753	12.571	11.375
5	3.7837	1.197	0.2658	8.5356	-1.8969	3.2341	0.2769	0.572	-0.6758	-0.4475	-0.2188	-0.1697	0.5403	-0.1593	-0.058	0.5884	-0.0349	-0.0612	0.2191	-0.1008	0.1212	20.6304	48.2996	83.8035
6	0.1222	-0.2683	0.0802	1.9509	0.1375	1.8772	0.0299	-0.0138	0.1184	-0.1366	0	-0.1562	0.109	-0.0999	-0.0298	0.1323	0.0054	0.0083	0.0395	0.0148	0.1523	21.9216	70.2717	97.3441
7	2.5536	-0.8413	0.7708	4.4815	1.5459	3.1415	-0.0371	-0.1434	0.2171	-0.018	0.1019	0.1221	0.5496	-0.0553	-0.0648	0.2649	-0.051	-0.0241	0.0764	0.0533	0.1673	18.0683	71.3615	94.4446
8	3.1543	-0.3217	-1.1549	5.4513	-1.4294	1.3969	0.1481	0.2131	0.0592	-0.434	-0.0471	0.0419	-0.0265	-0.1719	-0.101	0.1703	0.051	0.0244	0.0923	0.0208	0.0668	18.8014	80.1385	90.8574
9	5.2588	-3.9289	0.2266	4.1128	0.4943	2.9826	0.0736	0.1958	-0.4143	-0.0839	-0.1152	0.0681	0.3668	0.2002	0.0416	0.2718	0.0024	0.0106	0.0843	-0.0089	0.2537	9.472	1.7978	28.2341
10	0.4847	0.7668	0.6051	4.4989	1.8517	1.4636	0.0268	0.1255	0.1023	0.082	0.0224	-0.1132	0.0429	0.1282	-0.0492	0.0668	0.0156	-0.005	0.0729	0.0238	0.1375	15.976	18.1203	41.1337
11	9.3338	-3.1189	7.5453	1.1138	-2.5744	8.3657	0.6989	0.3484	-0.4383	-0.0859	-0.1281	-0.0224	0.3468	0.6107	-0.5708	0.4764	-0.0174	-0.2668	0.114	-0.0012	0.5331	22.9756	27.0394	52.1339
12	1.6777	0.6415	0.8825	2.6312	0.2997	1.456	0.0495	0.0814	0.0415	0.032	-0.0641	-0.0371	-0.0936	-0.0997	0.0146	0.0424	0.0178	0.0239	0.0385	0.0292	0.1483	14.4577	29.4831	40.4351
13	10.205	2.5774	3.564	6.6205	0.431	4.7079	0.1675	-0.4605	0.938	0.7709	-0.1456	0.5412	-0.4344	0.0996	-0.0218	0.6509	0.0044	0.1036	0.123	-0.0554	0.1342	20.411	86.4317	68.2306
14	0.4086	0.183	-0.3865	4.1072	0.6263	1.8453	0.016	-0.0069	-0.1189	0.1	0.0751	-0.2202	-0.2022	-0.0056	-0.0911	0.0961	-0.0082	0.0052	0.0352	0.0512	0.1372	22.4192	65.0391	54.6842
15	3.9064	-0.8723	-2.1886	3.1897	6.3163	12.6907	-0.0002	0.4954	-0.0588	0.0626	-0.2242	-0.0011	0.2269	-0.7182	0.2243	0.2761	-0.1709	0.002	0.2739	-0.0977	0.4014	11.3143	55.7652	49.7286
16	1.9017	0.4234	0.5524	4.0494	-1.9389	2.1329	0.1476	-0.0903	-0.0988	0.4776	-0.0532	0.0603	-0.1317	-0.2646	-0.0945	0.1186	-0.0158	0.0056	0.0799	0.0164	0.0892	19.1232	57.9247	61.9635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 30
2	X-RAY DIFFRACTION	2	A	31 - 62
3	X-RAY DIFFRACTION	3	A	63 - 190
4	X-RAY DIFFRACTION	4	A	191 - 239
5	X-RAY DIFFRACTION	5	B	6 - 47
6	X-RAY DIFFRACTION	6	B	48 - 167
7	X-RAY DIFFRACTION	7	B	168 - 197
8	X-RAY DIFFRACTION	8	B	198 - 239
9	X-RAY DIFFRACTION	9	C	4 - 39
10	X-RAY DIFFRACTION	10	C	40 - 117
11	X-RAY DIFFRACTION	11	C	118 - 131
12	X-RAY DIFFRACTION	12	C	132 - 239
13	X-RAY DIFFRACTION	13	D	6 - 46
14	X-RAY DIFFRACTION	14	D	47 - 160
15	X-RAY DIFFRACTION	15	D	161 - 177
16	X-RAY DIFFRACTION	16	D	178 - 239

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