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

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Basic information

Entry
Database: PDB / ID: 3cay
TitleCrystal structure of Lipopeptide Detergent (LPD-12)
ComponentsLPD-12
KeywordsDE NOVO PROTEIN / alpha helix / acyl chains / detergent / amphiphilic / lipopeptide / self-assembling peptide
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsHo, D.N. / Pomroy, N.C. / Cuesta-Seijo, J.A. / Prive, G.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structure of a self-assembling lipopeptide detergent at 1.20 A.
Authors: Ho, D.N. / Pomroy, N.C. / Cuesta-Seijo, J.A. / Prive, G.G.
History
DepositionFeb 20, 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)45,15034
Polymers33,91712
Non-polymers11,23422
Water7,422412
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)28,73920
Polymers22,6118
Non-polymers6,12712
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)32,82328
Polymers22,6118
Non-polymers10,21220
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)72.484, 130.040, 42.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 3350, 0.15 M potassium phosphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9793
ROTATING ANODEBRUKER AXS MICROSTAR21.54
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 4, 2006
Bruker Platinum 1352CCDJun 18, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystalSINGLE WAVELENGTHMx-ray1
2Helios multilayer opticsSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.541
ReflectionResolution: 1.2→50 Å / Num. all: 124528 / Num. obs: 124528 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.043
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.5 % / Rsym value: 0.244 / % possible all: 95.7

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1725 6284 Random
Rwork0.1344 --
all0.1364 119289 -
obs0.1364 119289 -
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 407 412 3170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03

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