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- PDB-3gud: Crystal structure of a novel intramolecular chaperon -

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Basic information

Entry
Database: PDB / ID: 3gud
TitleCrystal structure of a novel intramolecular chaperon
ComponentsNeck appendage protein
KeywordsCHAPERONE / 3-helix bundle / chaperon
Function / homology
Function and homology information


virus tail / identical protein binding
Similarity search - Function
Endosialidase, C-terminal domain superfamily / Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / DI(HYDROXYETHYL)ETHER / Neck appendage protein
Similarity search - Component
Biological speciesBacillus phage GA-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsSchulz, E.C. / Dickmanns, A. / Ficner, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Crystal structure of an intramolecular chaperone mediating triple-beta-helix folding.
Authors: Schulz, E.C. / Dickmanns, A. / Urlaub, H. / Schmitt, A. / Muhlenhoff, M. / Stummeyer, K. / Schwarzer, D. / Gerardy-Schahn, R. / Ficner, R.
History
DepositionMar 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Neck appendage protein
B: Neck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7346
Polymers30,4902
Non-polymers2444
Water1,53185
1
A: Neck appendage protein
hetero molecules

A: Neck appendage protein
hetero molecules

A: Neck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2939
Polymers45,7353
Non-polymers5586
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10070 Å2
ΔGint-36 kcal/mol
Surface area20310 Å2
MethodPISA
2
B: Neck appendage protein
hetero molecules

B: Neck appendage protein
hetero molecules

B: Neck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9109
Polymers45,7353
Non-polymers1756
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10030 Å2
ΔGint-112 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.040, 84.040, 41.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-20-

HOH

DetailsThe biological assembly is a Trimer generated from one monomer in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neck appendage protein


Mass: 15244.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage GA-1 (virus) / Gene: gene 12 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q9FZW3

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Non-polymers , 5 types, 89 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / pH: 4.8
Details: 25-30% PEG 2000, 0.1 M NaCitrate pH 4.8, 0.1 M (NH4)2SO4, temperature 293K.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.915
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.2→42 Å / Num. obs: 16515

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→42 Å / σ(F): 1.99 / Phase error: 29.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.232 829 5.02 %
Rwork0.197 --
obs0.199 16515 99.3 %
all-17344 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.37 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 10 85 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092038
X-RAY DIFFRACTIONf_angle_d1.3862748
X-RAY DIFFRACTIONf_dihedral_angle_d21.812753
X-RAY DIFFRACTIONf_chiral_restr0.11272
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.30050.36231000.39151910X-RAY DIFFRACTION98
2.3005-2.42180.35451040.29771971X-RAY DIFFRACTION98
2.4218-2.57350.32531040.29721984X-RAY DIFFRACTION98
2.5735-2.77220.29341040.291965X-RAY DIFFRACTION98
2.7722-3.05110.25041040.2611970X-RAY DIFFRACTION98
3.0511-3.49240.25421040.20351992X-RAY DIFFRACTION98
3.4924-4.39930.17891040.1411958X-RAY DIFFRACTION98
4.3993-42.02760.191020.13341939X-RAY DIFFRACTION98

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