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- PDB-3he4: Heterospecific coiled-coil pair SYNZIP5:SYNZIP6 -

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Basic information

Entry
Database: PDB / ID: 3he4
TitleHeterospecific coiled-coil pair SYNZIP5:SYNZIP6
Components
  • SYNZIP5
  • SYNZIP6
KeywordsDE NOVO PROTEIN / heterodimeric coiled-coil
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsReinke, A.W. / Grant, R.A. / Keating, A.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering.
Authors: Reinke, A.W. / Grant, R.A. / Keating, A.E.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNZIP6
B: SYNZIP5
C: SYNZIP6
D: SYNZIP5
E: SYNZIP6
F: SYNZIP5
G: SYNZIP6
H: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)47,2018
Polymers47,2018
Non-polymers00
Water99155
1
A: SYNZIP6
B: SYNZIP5
G: SYNZIP6
H: SYNZIP5

A: SYNZIP6
B: SYNZIP5
G: SYNZIP6
H: SYNZIP5

A: SYNZIP6
B: SYNZIP5
G: SYNZIP6
H: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)70,80212
Polymers70,80212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area22770 Å2
ΔGint-188 kcal/mol
Surface area33360 Å2
MethodPISA
2
A: SYNZIP6
B: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)11,8002
Polymers11,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-22 kcal/mol
Surface area7140 Å2
MethodPISA
3
C: SYNZIP6
D: SYNZIP5
E: SYNZIP6
F: SYNZIP5

C: SYNZIP6
D: SYNZIP5
E: SYNZIP6
F: SYNZIP5

C: SYNZIP6
D: SYNZIP5
E: SYNZIP6
F: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)70,80212
Polymers70,80212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area22580 Å2
ΔGint-189 kcal/mol
Surface area33620 Å2
MethodPISA
4
C: SYNZIP6
D: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)11,8002
Polymers11,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-22 kcal/mol
Surface area7250 Å2
MethodPISA
5
E: SYNZIP6
F: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)11,8002
Polymers11,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-21 kcal/mol
Surface area7170 Å2
MethodPISA
6
G: SYNZIP6
H: SYNZIP5


Theoretical massNumber of molelcules
Total (without water)11,8002
Polymers11,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-22 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.678, 82.678, 150.545
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUchain A and (resseq 15:48 )AA15 - 4817 - 50
21LYSLYSLEULEUchain C and (resseq 15:48 )CC15 - 4817 - 50
31LYSLYSLEULEUchain E and (resseq 15:48 )EE15 - 4817 - 50
41LYSLYSLEULEUchain G and (resseq 15:48 )GG15 - 4817 - 50
12THRTHRALAALAchain B and (resseq 2:40 )BB2 - 404 - 42
22THRTHRALAALAchain D and (resseq 2:40 )DD2 - 404 - 42
32THRTHRALAALAchain F and (resseq 2:40 )FF2 - 404 - 42
42THRTHRALAALAchain H and (resseq 2:40 )HH2 - 404 - 42

NCS ensembles :
ID
1
2

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Components

#1: Protein
SYNZIP6


Mass: 6359.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): RP3098
#2: Protein/peptide
SYNZIP5


Mass: 5441.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): RP3098
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 100 mM TRIS, 20% MPD, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.324
ReflectionResolution: 2.46→41.09 Å / Num. obs: 21204 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rsym value: 0.109 / Net I/σ(I): 26.346
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 5.4 % / Num. unique all: 2086 / Rsym value: 0.548 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→41.09 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.697 / σ(F): 0.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.258 1952 9.44 %
Rwork0.212 --
obs0.216 20684 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.212 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 60.986 Å2 / Biso min: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.177 Å20 Å2-0 Å2
2--0.177 Å2-0 Å2
3----0.354 Å2
Refinement stepCycle: LAST / Resolution: 2.46→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 55 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062952
X-RAY DIFFRACTIONf_angle_d0.6813944
X-RAY DIFFRACTIONf_chiral_restr0.043444
X-RAY DIFFRACTIONf_plane_restr0.002520
X-RAY DIFFRACTIONf_dihedral_angle_d14.8421156
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A268X-RAY DIFFRACTIONPOSITIONAL0.027
12C268X-RAY DIFFRACTIONPOSITIONAL0.027
13E268X-RAY DIFFRACTIONPOSITIONAL0.023
14G268X-RAY DIFFRACTIONPOSITIONAL0.03
21B326X-RAY DIFFRACTIONPOSITIONAL0.029
22D326X-RAY DIFFRACTIONPOSITIONAL0.029
23F326X-RAY DIFFRACTIONPOSITIONAL0.019
24H326X-RAY DIFFRACTIONPOSITIONAL0.027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.46-2.5440.3331770.29917331910
2.544-2.6460.3891810.29818071988
2.646-2.7660.3391870.30218422029
2.766-2.9120.281850.27418572042
2.912-3.0940.3151920.28218962088
3.094-3.3330.341950.25719162111
3.333-3.6680.2512040.21119222126
3.668-4.1990.1991980.17319162114
4.199-5.2880.2342040.17919202124
5.288-41.10.2281930.17719592152

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