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- PDB-1c4d: GRAMICIDIN CSCL COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c4d
TitleGRAMICIDIN CSCL COMPLEX
ComponentsGRAMICIDIN AGramicidin
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / DOUBLE HELIX / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / : / METHANOL / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SINGLE WAVELENGTH ANOMALOUS SCATTERING FROM CESIUM / Resolution: 2 Å
AuthorsWallace, B.A.
Citation
Journal: Science / Year: 1988
Title: The Gramicidin Pore: Crystal Structure of a Cesium Complex.
Authors: Wallace, B.A. / Ravikumar, K.
#1: Journal: Acta Crystallogr., Sect.B / Year: 1990
Title: The Use of Single-Wavelength Anomalous Scattering to Solve the Crystal Structure of a Gramicidin A/ Caesium Chloride Complex
Authors: Wallace, B.A. / Hendrickson, W.A. / Ravikumar, K.
History
DepositionJun 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2000Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _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

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Assembly

Deposited unit
A: GRAMICIDIN A
B: GRAMICIDIN A
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,22231
Polymers7,5294
Non-polymers1,69327
Water36020
1
A: GRAMICIDIN A
B: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,62716
Polymers3,7652
Non-polymers86214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GRAMICIDIN A
D: GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,59515
Polymers3,7652
Non-polymers83013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.118, 52.103, 31.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
GRAMICIDIN A / Gramicidin / VALYL GRAMICIDIN / Gramicidin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 1.73 Å3/Da / Density % sol: 31.67 %
Description: DATA EXHIBITED A HIGH MOSAIC SPREAD (1.5 - 2.0 DEGREES)
Crystal growDetails: 25 MG/ML GRAMICIDIN IN 53 MM CSCL IN METHANOL AT 10C FOR 3 MONTHS, BATCH METHOD, TEMPERATURE 283K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceWavelength: 1.54
DetectorType: PICKER FACS-1 / Detector: DIFFRACTOMETER / Date: May 1, 1983
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 3813 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2 %
Reflection shellResolution: 2→2.5 Å / Redundancy: 2 % / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHASITmodel building
ASCALCmodel building
X-PLORrefinement
HANSONET ALdata reduction
ANOSCLdata scaling
SCALE2data scaling
SCALE3data scaling
PHASITphasing
ASCALCphasing
RefinementMethod to determine structure: SINGLE WAVELENGTH ANOMALOUS SCATTERING FROM CESIUM
Resolution: 2→5 Å / Data cutoff high absF: 10 / Cross valid method: NONE / σ(F): 1
Details: INITIAL REFINEMENT REPORTED IN REFERENCES 1 & 2 USED PROLSQ
RfactorNum. reflection
Rwork0.232 -
obs0.232 3017
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 40 20 604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.042
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg5.14
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31.57
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d6.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2IONS.PARGRAM.TOP
X-RAY DIFFRACTION3IONS.TOP

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