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- PDB-1ec5: CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL -

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Basic information

Entry
Database: PDB / ID: 1ec5
TitleCRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL
ComponentsPROTEIN (FOUR-HELIX BUNDLE MODEL)
KeywordsDE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGeremia, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1999
Title: Tertiary Templates for the Design of Diiron Protein
Authors: Summa, C.M. / Lombardi, A. / Lewis, M. / Degrado, W.F.
#2: Journal: Annu.Rev.Biochem. / Year: 1999
Title: De Novo Design and Structural Characterization of Proteins and Metalloproteins
Authors: Degrado, W.F. / Summa, C.M. / Pavone, V. / Nastri, F. / Lombardi, A.
History
DepositionJan 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _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: PROTEIN (FOUR-HELIX BUNDLE MODEL)
B: PROTEIN (FOUR-HELIX BUNDLE MODEL)
C: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8096
Polymers17,6133
Non-polymers1963
Water57632
1
A: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules

A: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8734
Polymers11,7422
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: PROTEIN (FOUR-HELIX BUNDLE MODEL)
C: PROTEIN (FOUR-HELIX BUNDLE MODEL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8734
Polymers11,7422
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-99 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.070, 89.160, 79.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-59-

HOH

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Components

#1: Protein/peptide PROTEIN (FOUR-HELIX BUNDLE MODEL)


Mass: 5870.894 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: De novo protein design
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.82 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: CRYSTALS WERE GROWN FROM AN AMMONIUM SULFATE 2M SOLUTION, pH 4.6, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium acetate1reservoir
22.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.973
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 9, 1999 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.5→17.4 Å / Num. obs: 23396 / % possible obs: 96.2 % / Observed criterion σ(I): 4 / Redundancy: 5.2 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 10.7 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / Rsym value: 48 / % possible all: 96.7
Reflection
*PLUS
Num. obs: 4717 / % possible obs: 95.5 % / Num. measured all: 23396
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THEORETICAL MODEL

Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.304 204 5 %RANDOM
Rwork0.237 ---
obs-4474 95.48 %-
Displacement parametersBiso mean: 41.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 3 32 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1140.05
X-RAY DIFFRACTIONp_mcbond_it1.0862
X-RAY DIFFRACTIONp_mcangle_it1.843
X-RAY DIFFRACTIONp_scbond_it1.2892
X-RAY DIFFRACTIONp_scangle_it1.8713
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2150.3
X-RAY DIFFRACTIONp_multtor_nbd0.2980.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2310.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor29.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor54.820
X-RAY DIFFRACTIONp_special_tor

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