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- PDB-4fbs: Structure of monomeric NT from Euprosthenops australis Major Ampu... -

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Basic information

Entry
Database: PDB / ID: 4fbs
TitleStructure of monomeric NT from Euprosthenops australis Major Ampullate Spidroin 1 (MaSp1)
ComponentsMajor ampullate spidroin 1
KeywordsSTRUCTURAL PROTEIN / 5-helix bundle / pH regulation / spider silk assembly / Extracellular
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Spidroin, N-terminal domain / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Major ampullate spidroin 1
Similarity search - Component
Biological speciesEuprosthenops australis (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAskarieh, G. / Hedhammar, M. / Rising, A. / Johansson, J. / Knight, S.D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: pH-Dependent Dimerization of Spider Silk N-Terminal Domain Requires Relocation of a Wedged Tryptophan Side Chain
Authors: Jaudzems, K. / Askarieh, G. / Landreh, M. / Nordling, K. / Hedhammar, M. / Jornvall, H. / Rising, A. / Knight, S.D. / Johansson, J.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major ampullate spidroin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4303
Polymers14,2701
Non-polymers1602
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 33.244, 44.752
Angle α, β, γ (deg.)90.00, 115.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major ampullate spidroin 1


Mass: 14269.831 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 24-156 / Mutation: A72R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05H60
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis Tris propane pH 6.5, 0.25M NaBr, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2011 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.7→40.44 Å / Num. all: 12695 / Num. obs: 12385 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 5.2 / % possible all: 80.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: dev_1041)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial NMR model of NT A72R

Resolution: 1.7→40.435 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 611 4.93 %Random
Rwork0.1421 ---
all0.1448 12695 --
obs0.1448 12384 97.56 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 2 122 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01995
X-RAY DIFFRACTIONf_angle_d1.2281372
X-RAY DIFFRACTIONf_dihedral_angle_d13.173381
X-RAY DIFFRACTIONf_chiral_restr0.066163
X-RAY DIFFRACTIONf_plane_restr0.005183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7-1.87110.24121570.1462710286791
1.8711-2.14190.20691590.125529823141100
2.1419-2.69850.19361410.134630113152100
2.6985-40.44640.18291540.15113070322499

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