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- PDB-4l37: SP2-SP3 - a complex of two storage proteins from Bombyx mori hemolymph -

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Basic information

Entry
Database: PDB / ID: 4l37
TitleSP2-SP3 - a complex of two storage proteins from Bombyx mori hemolymph
Components
  • Arylphorin
  • Silkworm storage protein
KeywordsPROTEIN BINDING / arylphorin / hemocyanin-like fold / storage proteins / BmSP2 / BmSP3 / hemolymph
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain ...Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Di-copper centre-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
THIOCYANATE ION / Silkworm storage protein / Arylphorin
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPietrzyk, A.J. / Bujacz, A. / Mueller-Dieckmann, J. / Jaskolski, M. / Bujacz, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Crystallographic identification of an unexpected protein complex in silkworm haemolymph.
Authors: Pietrzyk, A.J. / Bujacz, A. / Mueller-Dieckmann, J. / ochynska, M. / Jaskolski, M. / Bujacz, G.
History
DepositionJun 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Silkworm storage protein
B: Arylphorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,63514
Polymers163,2622
Non-polymers2,37312
Water2,450136
1
A: Silkworm storage protein
B: Arylphorin
hetero molecules

A: Silkworm storage protein
B: Arylphorin
hetero molecules

A: Silkworm storage protein
B: Arylphorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,90542
Polymers489,7866
Non-polymers7,11936
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area43650 Å2
ΔGint-308 kcal/mol
Surface area136160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.750, 192.750, 180.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-802-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Silkworm storage protein / Uncharacterized protein


Mass: 81283.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: H9JHM9
#2: Protein Arylphorin / Uncharacterized protein


Mass: 81978.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: Q1HPP4

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Sugars , 1 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 146 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M ammonium sulfate 0.02 M sodium thiocyanate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2012 / Details: mirrors
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.9→48 Å / Num. all: 44365 / Num. obs: 44232 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 43.07 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 23.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 5 / Num. unique all: 4198 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWJ

3gwj


Resolution: 2.9→48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.091 / SU ML: 0.251 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22267 1096 2.5 %RANDOM
Rwork0.16582 ---
all0.16726 44365 --
obs0.16726 43121 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.406 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å21.49 Å2-0 Å2
2--1.49 Å2-0 Å2
3----4.83 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11373 0 150 136 11659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211920
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.95616151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92451343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56424.025646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.878151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2811546
X-RAY DIFFRACTIONr_chiral_restr0.1150.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219340
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 75 -
Rwork0.252 3129 -
obs--100 %
Refinement TLS params.

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

IDL11 (°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)
10.4325-0.0678-0.01490.47010.13890.6311-0.0505-0.0442-0.00820.03110.0822-0.00810.0064-0.1282-0.03170.02010.02770.00990.14620.01950.073853.706947.9809116.4785
20.2733-0.0215-0.03830.3435-0.06620.2189-0.0164-0.00460.01620.04140.00350.00640.027-0.00930.01290.05140.01290.00310.06610.00360.09676.18242.5732106.8249
30.4095-0.36890.19290.4073-0.07060.35280.02650.0183-0.03770.02410.00320.0580.1596-0.0038-0.02970.1266-0.02170.01470.0229-0.0020.095171.682421.7925109.4861
40.6157-0.12580.08340.49980.24661.19260.03370.09830.035-0.0565-0.0138-0.01440.0861-0.2118-0.01990.0456-0.0236-0.03670.1656-0.00190.056653.780149.714562.3352
50.2997-0.1111-0.1350.06410.03640.2071-0.00090.0424-0.0078-0.01880.010.0015-0.0272-0.0327-0.00910.06410.0189-0.01590.10220.01410.084873.223762.367472.7835
60.19070.2197-0.18010.4243-0.13230.2392-0.00230.03120.0418-0.0611-0.01830.0263-0.0314-0.05040.02060.08430.0773-0.02640.09660.02620.119462.486380.678169.1112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 153
2X-RAY DIFFRACTION2A154 - 438
3X-RAY DIFFRACTION3A439 - 679
4X-RAY DIFFRACTION4B10 - 156
5X-RAY DIFFRACTION5B157 - 441
6X-RAY DIFFRACTION6B442 - 675

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