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- PDB-5iz2: Crystal structure of the N. clavipes spidroin NTD at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 5iz2
TitleCrystal structure of the N. clavipes spidroin NTD at pH 6.5
Components
  • Major ampullate spidroin 1A
  • Major ampullate spidroin 1A (Partial C-terminus)
KeywordsSTRUCTURAL PROTEIN / spidroin / major ampullate / homodimer
Function / homologySpidroin, 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 / Major ampullate spidroin 1A
Function and homology information
Biological speciesNephila clavipes (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsAtkison, J.H. / Olsen, S.K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of the Nephila clavipes Major Ampullate Spidroin 1A N-terminal Domain Reveals Plasticity at the Dimer Interface.
Authors: Atkison, J.H. / Parnham, S. / Marcotte, W.R. / Olsen, S.K.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Major ampullate spidroin 1A
A: Major ampullate spidroin 1A
Z: Major ampullate spidroin 1A (Partial C-terminus)


Theoretical massNumber of molelcules
Total (without water)30,2763
Polymers30,2763
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-24 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.480, 67.480, 90.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Major ampullate spidroin 1A


Mass: 14975.525 Da / Num. of mol.: 2 / Fragment: unp residues 24-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila clavipes (spider) / Gene: MaSp1A / Plasmid: pGEX-6P2 / Details (production host): GST fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: B5SYS5
#2: Protein/peptide Major ampullate spidroin 1A (Partial C-terminus)


Mass: 325.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chain Z consists of three residues thought to be part of the C-terminus of either Chain A or Chain B and is not a separate chain. It is unclear as to which chain these residues belong
Source: (gene. exp.) Nephila clavipes (spider) / Gene: MaSp1A / Plasmid: pGEX-6P2 / Details (production host): GST fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: B5SYS5*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors have indicated that they don't know whether chain Z belongs to A or B chain. Ser-Tyr-Gly of ...Authors have indicated that they don't know whether chain Z belongs to A or B chain. Ser-Tyr-Gly of chain Z represents a C-terminal portion of entity belonging to B and A

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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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: Cubic
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M BIS-TRIS, 29% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→100 Å / Num. obs: 16120 / % possible obs: 98.23 % / Redundancy: 10.81 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.71
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 11.06 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.57 / % possible all: 94.32

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L2R

3l2r


Resolution: 2.02→35.741 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 18.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1561 9.87 %random selection
Rwork0.1644 ---
obs0.1685 15808 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→35.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 120 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041866
X-RAY DIFFRACTIONf_angle_d0.7242515
X-RAY DIFFRACTIONf_dihedral_angle_d11.492667
X-RAY DIFFRACTIONf_chiral_restr0.031288
X-RAY DIFFRACTIONf_plane_restr0.003332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.08520.23251320.16911227X-RAY DIFFRACTION95
2.0852-2.15970.22421430.16011220X-RAY DIFFRACTION95
2.1597-2.24610.20271400.15231277X-RAY DIFFRACTION97
2.2461-2.34830.21881340.15851270X-RAY DIFFRACTION98
2.3483-2.47210.2371400.16221264X-RAY DIFFRACTION98
2.4721-2.6270.21871440.17531284X-RAY DIFFRACTION99
2.627-2.82970.231410.17611323X-RAY DIFFRACTION100
2.8297-3.11430.20731400.17851308X-RAY DIFFRACTION100
3.1143-3.56460.22061420.16641327X-RAY DIFFRACTION100
3.5646-4.48970.17871480.14491350X-RAY DIFFRACTION100
4.4897-35.74680.18331570.17131397X-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)
10.1117-0.04430.14560.221-0.01630.23120.06740.04260.10550.02350.02470.0756-0.1717-0.04050.02710.21410.066-0.01790.19070.01560.233921.05718.04547.9963
21.35910.04840.57620.27380.36430.874-0.0431-0.26670.02230.0271-0.1095-0.2187-0.0349-0.0893-0.35070.20570.0572-0.02530.12330.06390.261927.096411.429115.1556
30.0514-0.0559-0.00211.45621.17471.05350.15640.3225-0.134-0.43120.1899-0.362-0.17440.14790.42980.25610.0352-0.03760.2157-0.00080.25226.73178.68835.8221
40.2528-0.17810.01620.13980.03790.0714-0.0447-0.21430.02160.0090.10940.17980.0894-0.0820.00020.24330.0344-0.03460.2850.02710.239911.979212.86336.3468
50.83710.6488-0.29272.5392-0.59920.18920.09920.2574-0.4451-0.3655-0.011-0.12640.1333-0.0560.15730.17530.0448-0.12840.1116-0.02390.172714.88915.91380.1433
60.00530.00640.00230.0063-0.00050.00550.0392-0.1286-0.0704-0.0090.04990.0206-0.1226-0.003200.22320.0022-0.03660.19130.00250.237322.2745-8.834120.2209
70.3648-0.1860.19230.35360.23860.42430.21430.0920.171-0.0505-0.0382-0.2637-0.04240.00690.0770.22850.0471-0.00540.1330.02160.201234.358-0.845415.1999
81.6634-0.5169-0.14740.17470.0850.02130.13890.69910.0472-0.3422-0.1401-0.0292-0.0161-0.0907-0.01410.32470.0343-0.05060.2811-0.01650.235929.3565-4.88916.9919
90.1909-0.0221-0.08160.0512-0.02460.07660.0430.4353-0.0752-0.2206-0.04480.102-0.2387-0.03060.13430.52680.0099-0.33350.5224-0.10130.230522.7849-6.27262.312
100.00840.01870.00090.0421-0.0010.00520.0346-0.0201-0.01980.04740.07250.08070.0737-0.08530.00040.44930.1288-0.140.70330.1080.53112.077214.20028.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 34 )
2X-RAY DIFFRACTION2chain 'B' and (resid 35 through 58 )
3X-RAY DIFFRACTION3chain 'B' and (resid 59 through 83 )
4X-RAY DIFFRACTION4chain 'B' and (resid 84 through 109 )
5X-RAY DIFFRACTION5chain 'B' and (resid 110 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 6 through 12 )
7X-RAY DIFFRACTION7chain 'A' and (resid 13 through 62 )
8X-RAY DIFFRACTION8chain 'A' and (resid 63 through 109 )
9X-RAY DIFFRACTION9chain 'A' and (resid 110 through 128 )
10X-RAY DIFFRACTION10chain 'Z' and (resid -5 through -3 )

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