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- PDB-3pub: Crystal structure of the Bombyx mori low molecular weight lipopro... -

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Basic information

Entry
Database: PDB / ID: 3pub
TitleCrystal structure of the Bombyx mori low molecular weight lipoprotein 7 (Bmlp7)
Components30kDa protein
KeywordsUNKNOWN FUNCTION / beta-trefoil fold / haemolymph
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Lepidopteran low molecular weight (30 kD) lipoprotein, N-terminal domain / Lepidopteran low molecular weight lipoprotein / Lepidopteran low molecular weight lipoprotein, N-terminal domain / Lepidopteran low molecular weight (30 kD) lipoprotein / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsYang, J.-P. / Ma, X.-X. / He, Y.-X. / Li, W.-F. / Kang, Y. / Bao, R. / Chen, Y. / Zhou, C.-Z.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of the 30 K protein from the silkworm Bombyx mori reveals a new member of the beta-trefoil superfamily
Authors: Yang, J.-P. / Ma, X.-X. / He, Y.-X. / Li, W.-F. / Kang, Y. / Bao, R. / Chen, Y. / Zhou, C.-Z.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30kDa protein
B: 30kDa protein


Theoretical massNumber of molelcules
Total (without water)57,9292
Polymers57,9292
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.855, 49.322, 54.790
Angle α, β, γ (deg.)93.26, 94.04, 103.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 30kDa protein / low molecular weight lipoprotein 7


Mass: 28964.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: E5EVW2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (pH 7.5), 0.2M KCl, 28% pentaerythritol propoxylate (17/8, PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 31866 / % possible obs: 96.8 %
Reflection shellResolution: 1.91→1.94 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→47.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.315 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23506 1602 5 %RANDOM
Rwork0.1925 ---
obs0.19464 30258 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.828 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.49 Å21.26 Å2
2---0.54 Å2-0.58 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 0 93 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9365317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98924.356202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91415680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1521522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023022
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6511.52335
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2223751
X-RAY DIFFRACTIONr_scbond_it2.03831596
X-RAY DIFFRACTIONr_scangle_it3.2174.51566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.909→1.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 142 -
Rwork0.197 2205 -
obs--94.68 %
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)
11.82310.2367-0.30521.8182-0.381.5970.0167-0.09630.05590.1912-0.01170.1534-0.04360.0091-0.0050.10910.0001-0.00090.0966-0.00640.1073-12.3858.12321.639
20.9326-0.1746-0.45530.88480.41071.2165-0.01110.1323-0.03910.0037-0.03980.01530.031-0.02520.05090.08010.0017-0.02860.1293-0.00130.0922-0.096-0.120.537
31.2994-0.3946-0.2311.86640.47492.340.02560.0196-0.0525-0.1431-0.0221-0.1164-0.01450.0065-0.00340.0890.0033-0.00080.0798-0.00410.124428.689-18.266-45.873
40.953-0.2103-0.95050.58280.38362.2342-0.04780.0381-0.02130.0980.0244-0.02660.0911-0.16680.02340.08450.0053-0.02830.11640.0020.0915.494-10.692-24.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 126
2X-RAY DIFFRACTION2A127 - 284
3X-RAY DIFFRACTION3B50 - 126
4X-RAY DIFFRACTION4B127 - 285

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