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- PDB-4efp: Bombyx mori lipoprotein 7 isolated from its natural source at 1.3... -

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Basic information

Entry
Database: PDB / ID: 4efp
TitleBombyx mori lipoprotein 7 isolated from its natural source at 1.33 A resolution
Components30kDa protein
KeywordsUNKNOWN FUNCTION / VHS domain / beta-trefoil
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 / TRIETHYLENE GLYCOL / THIOCYANATE ION / 30K protein 2
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.33 Å
AuthorsPietrzyk, A.J. / Panjikar, S. / Bujacz, A. / Mueller-Dieckmann, J. / Jaskolski, M. / Bujacz, G.
CitationJournal: 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
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,08214
Polymers55,1582
Non-polymers92412
Water9,926551
1
A: 30kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1258
Polymers27,5791
Non-polymers5467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 30kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9576
Polymers27,5791
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.211, 49.993, 55.244
Angle α, β, γ (deg.)93.41, 94.70, 102.78
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 30kDa protein


Mass: 27579.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: protein isolated from fifth instar larvae / Source: (natural) Bombyx mori (domestic silkworm) / References: UniProt: E5EVW2

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Non-polymers , 7 types, 563 molecules

#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2010
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.33→23 Å / Num. all: 94702 / Num. obs: 94674 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.66
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.42 / % possible all: 78.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-RickshawMR-SAD protocolphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.33→23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.25 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23058 1223 1.3 %RANDOM
Rwork0.18357 ---
all0.18417 94702 --
obs0.18417 93451 93.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0.49 Å20.41 Å2
2---0.59 Å2-0.03 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.33→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 43 551 4430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224161
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9565652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39924.36211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71815749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.751525
X-RAY DIFFRACTIONr_chiral_restr0.2190.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023195
X-RAY DIFFRACTIONr_mcbond_it2.2361.52430
X-RAY DIFFRACTIONr_mcangle_it3.18823943
X-RAY DIFFRACTIONr_scbond_it4.67831731
X-RAY DIFFRACTIONr_scangle_it6.0824.51679
X-RAY DIFFRACTIONr_rigid_bond_restr2.25734161
LS refinement shellResolution: 1.33→1.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 68 -
Rwork0.188 5348 -
obs--71.67 %

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