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- PDB-4iy8: Bmlp3 - P21 crystal form -

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Basic information

Entry
Database: PDB / ID: 4iy8
TitleBmlp3 - P21 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
DI(HYDROXYETHYL)ETHER / 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: 2.36 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
C: 30K protein 1
D: 30K protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8416
Polymers110,4524
Non-polymers3882
Water3,963220
1
A: 30K protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8952
Polymers27,6131
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
3
C: 30K protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7192
Polymers27,6131
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 30K protein 1


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 124.410, 67.890
Angle α, β, γ (deg.)90.00, 114.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
30K protein 1


Mass: 27613.082 Da / Num. of mol.: 4 / 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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 550, 0.1 M CaCl2, 0.1 M Bis-Tris, pH 6.5, 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: Mar 6, 2011 / 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: 2.36→34.4 Å / Num. all: 35358 / Num. obs: 35189 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.7
Reflection shellResolution: 2.36→2.46 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.74 / Num. unique all: 4096 / % possible all: 99.7

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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 4EFP

4efp


Resolution: 2.36→33.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.207 / SU ML: 0.242 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.868 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1106 3.1 %RANDOM
Rwork0.17312 ---
obs0.17578 34081 99.78 %-
all-35358 --
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: 40.639 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å2-0.92 Å2
2--3.92 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.36→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 26 220 8038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198038
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.93710889
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2125960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81824.31420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.873151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0551549
X-RAY DIFFRACTIONr_chiral_restr0.1220.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216219
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 83 -
Rwork0.288 2502 -
obs--99.85 %
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)
117.61961.83945.3610.48610.7782.96610.3319-0.40490.2644-0.0767-0.1903-0.11830.059-0.2015-0.14160.12250.05820.04340.11390.02780.1289-4.19394.081524.2104
22.44440.0176-0.80930.07950.12371.1314-0.08120.0027-0.1526-0.05240.01030.0390.0883-0.08730.07080.1379-0.00670.01360.0471-0.01060.152811.2973-3.011414.5106
31.0481-0.3930.1331.45740.31050.9587-0.0336-0.0798-0.1466-0.0526-0.0039-0.11590.05420.10340.03740.13210.01380.01110.03610.00170.131529.1568-2.471712.2403
41.55530.2457-0.77572.12070.10171.24730.0362-0.00980.0625-0.11180.037-0.0844-0.1008-0.1048-0.07320.1435-0.00160.00090.05170.02350.109324.41345.89910.9083
512.9024-0.1733-2.5250.41310.74131.7382-0.01320.23410.00050.0570.0162-0.0090.1031-0.0661-0.0030.0715-0.0007-0.02930.10830.02490.1329-5.888531.5043-9.6028
63.2767-0.83971.11770.5071-0.29830.76840.0256-0.04570.10210.042-0.00850.0542-0.0511-0.0946-0.01720.12310.0020.02720.04330.02240.13589.418138.46320.1125
71.1049-0.03730.6331.9111-0.37241.7059-0.0190.01760.11490.1798-0.0517-0.2427-0.1583-0.06780.07070.1386-0.0175-0.03380.03620.01260.123827.742837.55942.7464
80.4072-0.69350.3291.9619-0.70050.4698-0.0147-0.0628-0.0582-0.02070.0691-0.0504-0.0118-0.0679-0.05430.1205-0.0022-0.02980.10560.03010.132522.729529.18223.6933
910.4637-0.4034-2.86981.3609-0.38231.38260.123-0.3346-0.11150.0882-0.0341-0.061-0.01860.0739-0.08890.08120.0162-0.02840.1336-0.03950.136726.067230.219440.939
102.56830.57710.88640.28680.09840.59260.00660.2069-0.0386-0.10310.0303-0.0438-0.03750.1429-0.0370.13520.01090.01880.1395-0.02860.095710.822835.140330.0634
111.8490.13110.4161.00050.97811.45930.08440.12710.1057-0.0415-0.08080.1498-0.09640.0956-0.00360.135-0.0125-0.03270.12-0.0110.1434-7.670533.957728.0931
121.95780.55551.18020.94040.47470.74220.23090.0316-0.28450.0939-0.0155-0.01690.1760.0181-0.21540.17490.0186-0.09680.0786-0.01440.1804-2.380125.23928.5176
135.06592.1184-0.69361.150.09090.66190.0093-0.1570.0007-0.0474-0.0174-0.0074-0.06690.00670.00810.06020.0070.01620.24660.00750.041527.84564.733-26.2091
144.4305-0.1866-1.95470.80830.39961.1999-0.053-0.5176-0.3362-0.0191-0.0875-0.0683-0.00420.24810.14050.00490.02010.00520.29710.07180.037712.6946-0.6527-15.4767
152.7413-0.4205-1.28571.3148-0.5691.8325-0.1434-0.2936-0.37160.0597-0.06670.19650.01590.14590.21010.08070.02150.01380.14280.00750.0906-5.58350.5364-13.012
162.8522-0.5734-0.59691.13190.95511.22970.1251-0.41940.1965-0.1393-0.07070.0868-0.19660.1614-0.05440.0842-0.04360.02630.2737-0.07840.068-0.39729.3164-13.2209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 22
2X-RAY DIFFRACTION2A23 - 113
3X-RAY DIFFRACTION3A114 - 171
4X-RAY DIFFRACTION4A172 - 239
5X-RAY DIFFRACTION5B1 - 22
6X-RAY DIFFRACTION6B23 - 112
7X-RAY DIFFRACTION7B113 - 171
8X-RAY DIFFRACTION8B172 - 239
9X-RAY DIFFRACTION9C1 - 22
10X-RAY DIFFRACTION10C23 - 112
11X-RAY DIFFRACTION11C113 - 172
12X-RAY DIFFRACTION12C173 - 239
13X-RAY DIFFRACTION13D1 - 22
14X-RAY DIFFRACTION14D23 - 112
15X-RAY DIFFRACTION15D113 - 172
16X-RAY DIFFRACTION16D173 - 239

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