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- PDB-4iy9: Bmlp3 - C2 crystal form -

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Basic information

Entry
Database: PDB / ID: 4iy9
TitleBmlp3 - C2 crystal form
Components30K protein 1
KeywordsLIPID BINDING PROTEIN / Lipoprotein 11 family / hemolymph
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
IODIDE ION / Low molecular mass lipoprotein 3 / Low molecular mass lipoprotein 3
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPietrzyk, A.J. / Bujacz, A. / Mueller-Dieckmann, J. / Jaskolski, M. / Bujacz, G.
CitationJournal: Plos One / Year: 2013
Title: Two Crystal Structures of Bombyx mori Lipoprotein 3 - Structural Characterization of a New 30-kDa Lipoprotein Family Member.
Authors: Pietrzyk, A.J. / Bujacz, A. / Mueller-Dieckmann, J. / Lochynska, M. / Jaskolski, M. / Bujacz, G.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30K protein 1
B: 30K protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3533
Polymers55,2262
Non-polymers1271
Water2,234124
1
A: 30K protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7402
Polymers27,6131
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 30K protein 1


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.150, 34.560, 93.140
Angle α, β, γ (deg.)90.00, 97.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 30K protein 1


Mass: 27613.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: protein isolated from hemolymph / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: H9J4F6, UniProt: Q00802*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M (NH4)2SO4, 0.1 M NH4I, 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: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 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: 2.1→38.164 Å / Num. all: 29081 / Num. obs: 26553 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.1841 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.58 / Num. unique all: 3770 / % possible all: 86.3

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EFP

4efp


Resolution: 2.1→38.1 Å / SU ML: 0.36 / Isotropic thermal model: isotropic / σ(F): 1.35 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 1325 5 %RANDOM
Rwork0.2161 ---
obs0.2188 26475 91.08 %-
all-29081 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 1 124 3967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193979
X-RAY DIFFRACTIONf_angle_d1.815402
X-RAY DIFFRACTIONf_dihedral_angle_d16.4491470
X-RAY DIFFRACTIONf_chiral_restr0.105563
X-RAY DIFFRACTIONf_plane_restr0.01697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.39611390.32392617X-RAY DIFFRACTION86
2.1841-2.28350.4663690.42531330X-RAY DIFFRACTION44
2.2835-2.40390.39341530.27972892X-RAY DIFFRACTION97
2.4039-2.55440.37491590.27743017X-RAY DIFFRACTION99
2.5544-2.75160.36371590.26623025X-RAY DIFFRACTION99
2.7516-3.02840.28811590.23863021X-RAY DIFFRACTION99
3.0284-3.46640.27081600.21583040X-RAY DIFFRACTION99
3.4664-4.36630.20381600.17153050X-RAY DIFFRACTION98
4.3663-38.17010.22271670.17763158X-RAY DIFFRACTION99
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)
11.8776-0.48660.16931.63950.14952.07550.13741.4040.0856-0.5452-0.05130.28850.2008-0.8353-0.13990.38520.0097-0.02210.93040.06940.39811.37729.0116-22.3078
22.5366-0.55740.3952.3426-1.80643.078-0.0693-0.3505-0.0644-0.03250.54220.29650.088-1.2093-0.19410.2462-0.0011-0.03410.58770.12960.353611.35017.33822.1569
32.7026-0.37691.34360.7645-0.30763.335-0.0149-0.66160.14470.20150.1857-0.1405-0.3025-0.4238-0.06550.23150.0630.01720.16850.05770.286421.2667.33247.8869
42.0098-0.07620.48391.6018-0.99253.62660.2047-0.0985-0.4933-0.14210.25240.22930.7567-0.436-0.14190.2985-0.05-0.06180.27120.16620.387216.361-2.85773.5612
53.0986-0.56110.68280.9694-0.09232.20690.0665-1.18590.0254-0.1326-0.0676-0.3415-0.07330.6970.02740.664-0.03810.02411.0865-0.27990.542149.99550.352155.2712
62.08070.5702-0.03151.86540.14012.18820.257-0.94990.05770.0115-0.1782-0.26320.1382-0.0978-0.09280.3956-0.0051-0.03640.9779-0.16710.430250.2304-4.132547.1216
71.720.00030.14140.30140.01471.1080.3444-0.4409-0.26971.04280.1447-0.12050.26021.0442-0.20870.4874-0.0159-0.05990.7222-0.00740.367748.5929-10.395334.0742
81.8274-0.17320.22911.27561.17671.0578-0.06310.7598-0.616-0.32810.1253-0.1785-0.2360.0059-0.07890.26030.1058-0.01880.09780.12420.359738.4102-10.797917.3816
93.3011-0.74360.43850.583-0.81243.38370.0735-0.20720.29460.19870.2078-0.1992-0.05160.3966-0.18330.2379-0.01780.06390.154-0.02890.302844.0007-5.445224.9293
100.7325-1.0295-0.27211.62730.78762.69030.1651-0.27430.3825-0.16160.1867-0.0544-0.5042-0.4033-0.31740.34570.04460.04810.37120.06560.302332.04980.357121.8012
113.61910.01390.19582.9372-0.42312.91310.1991-0.499-0.03190.3716-0.01620.00520.1717-0.2759-0.12330.268-0.00720.00150.28070.0680.231534.0144-10.198731.9557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5:51 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 52:124 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 125:175 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 176:239 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 5:35 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 36:76 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 77:94 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 95:114 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 115:155 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 156:179 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 180:239 )

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