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- PDB-4zn8: Using molecular dynamics simulations to predict domain swapping o... -

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Basic information

Entry
Database: PDB / ID: 4zn8
TitleUsing molecular dynamics simulations to predict domain swapping of computationally designed protein variants
Componentscomputationally modified engrailed homeodomain
KeywordsDE NOVO PROTEIN / computational protein design / domain-swapped dimer
Function / homology:
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsHuang, P.-S. / Thomas, L.M. / Mayo, S.L.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.
Authors: Mou, Y. / Huang, P.S. / Thomas, L.M. / Mayo, S.L.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.type ..._citation.journal_id_CSD / _diffrn_detector.type / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: computationally modified engrailed homeodomain
B: computationally modified engrailed homeodomain
C: computationally modified engrailed homeodomain
D: computationally modified engrailed homeodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9068
Polymers26,7504
Non-polymers1564
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-55 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.456, 62.682, 76.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
computationally modified engrailed homeodomain


Mass: 6687.403 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG3350, 0.2 M potassium phosphate, 0.1 M Tris, pH 7.0
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2004
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→39.778 Å / Num. all: 5289 / Num. obs: 5197 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZO1.97.7data reduction
SCALEPACK1.97.7data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→39 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3121 251 4.83 %RANDOM
Rwork0.2495 ---
obs0.2527 5192 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 4 0 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031795
X-RAY DIFFRACTIONf_angle_d0.6282382
X-RAY DIFFRACTIONf_dihedral_angle_d15.571736
X-RAY DIFFRACTIONf_chiral_restr0.022229
X-RAY DIFFRACTIONf_plane_restr0.002314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.77920.29951130.25572405X-RAY DIFFRACTION98
3.7792-39.77510.31891380.24542536X-RAY DIFFRACTION98

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