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- PDB-3cba: Crystal structure of Lipopeptide Detergent (LPD-12) (Hexagonal) -

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Basic information

Entry
Database: PDB / ID: 3cba
TitleCrystal structure of Lipopeptide Detergent (LPD-12) (Hexagonal)
ComponentsLPD-12
KeywordsDE NOVO PROTEIN / alpha helix / acyl chains / detergent / amphiphilic / lipopeptide / self-assembling peptide
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHo, D.N. / Pomroy, N.C. / Cuesta-Seijo, J.A. / Prive, G.G.
CitationJournal: To be Published
Title: Packing and Twinning in Orthorhombic and Hexagonal Crystals of Lipopeptide Detergent (LPD-12)
Authors: Ho, D.N. / Pomroy, N.C. / Cuesta-Seijo, J.A. / Prive, G.G.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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: LPD-12
B: LPD-12
C: LPD-12
D: LPD-12
E: LPD-12
F: LPD-12
G: LPD-12
H: LPD-12
I: LPD-12
J: LPD-12
K: LPD-12
L: LPD-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,63828
Polymers33,91712
Non-polymers7,72116
Water4,179232
1
A: LPD-12
B: LPD-12
C: LPD-12
D: LPD-12
E: LPD-12
F: LPD-12
G: LPD-12
H: LPD-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,95417
Polymers22,6118
Non-polymers4,3439
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: LPD-12
J: LPD-12
K: LPD-12
L: LPD-12
hetero molecules

I: LPD-12
J: LPD-12
K: LPD-12
L: LPD-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,36722
Polymers22,6118
Non-polymers6,75614
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)127.261, 127.261, 42.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein/peptide
LPD-12


Mass: 2826.394 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: de novo designed lipopeptide
#2: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 3350, 0.15M potassium phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2004
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 43769 / Num. obs: 43769 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rsym value: 0.053
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rsym value: 0.26 / % possible all: 98.4

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2434 2174 Random
Rwork0.1843 --
all0.1874 41386 -
obs0.1874 41386 -
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 276 232 2788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.02

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