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- PDB-1mft: Crystal Structure Of Four-Helix Bundle Model -

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Basic information

Entry
Database: PDB / ID: 1mft
TitleCrystal Structure Of Four-Helix Bundle Model
ComponentsFour-helix bundle model
KeywordsDE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN / HELIX TURN HELIX
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLahr, S.J. / Stayrook, S.E. / North, B. / Kaplan, J. / Geremia, S. / DeGrado, W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Analysis and Design of Turns in alpha-Helical Hairpins
Authors: Lahr, S.J. / Engel, D.E. / Stayrook, S.E. / Maglio, O. / North, B. / Geremia, S. / Lombardi, A. / DeGrado, W.F.
History
DepositionAug 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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.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

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Assembly

Deposited unit
A: Four-helix bundle model
B: Four-helix bundle model
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0864
Polymers12,9552
Non-polymers1312
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-101 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.233, 54.810, 37.168
Angle α, β, γ (deg.)90.00, 105.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Four-helix bundle model / due ferri (II) turn mutant


Mass: 6477.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 300, zinc chloride, bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
226 %(w/v)PEG3001reservoir
40.1 MHEPES1reservoirpH6.0
31reservoirtwofold excessZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.605 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2001 / Details: 27-pole hybrid wiggler
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.605 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 3444 / Num. obs: 3229 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3 / Num. unique all: 268 / Rsym value: 0.217 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 7203 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
MADNESSdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EC5

1ec5


Resolution: 2.5→18.21 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 336592.54 / Data cutoff high rms absF: 336592.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 224 7 %RANDOM
Rwork0.222 ---
all0.227 3229 --
obs0.222 3199 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0375 Å2 / ksol: 0.389022 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-10.24 Å20 Å2-5.93 Å2
2---3.39 Å20 Å2
3----6.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 2 13 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.311.5
X-RAY DIFFRACTIONc_mcangle_it3.512
X-RAY DIFFRACTIONc_scbond_it6.182
X-RAY DIFFRACTIONc_scangle_it8.052.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 41 7.6 %
Rwork0.255 496 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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