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- PDB-5c21: Crystal structure of native HlyD from E. coli -

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Basic information

Entry
Database: PDB / ID: 5c21
TitleCrystal structure of native HlyD from E. coli
ComponentsChromosomal hemolysin D
KeywordsPROTEIN TRANSPORT / ABC transporter / HlyD
Function / homology
Function and homology information


protein secretion by the type I secretion system / protein secretion / killing of cells of another organism / plasma membrane
Similarity search - Function
Secretion protein HlyD, conserved site / Type I secretion membrane fusion protein, HlyD family / HlyD family secretion proteins signature. / HlyD family secretion protein / :
Similarity search - Domain/homology
Membrane fusion protein (MFP) family protein / Hemolysin secretion protein D, chromosomal
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsHa, N.C. / Kim, J.S. / Yoon, B.Y.
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria
Authors: Kim, J.S. / Song, S. / Lee, M. / Lee, S. / Lee, K. / Ha, N.C.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosomal hemolysin D
B: Chromosomal hemolysin D


Theoretical massNumber of molelcules
Total (without water)64,3952
Polymers64,3952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-10 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.615, 93.173, 163.388
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 Chromosomal hemolysin D


Mass: 32197.725 Da / Num. of mol.: 2 / Fragment: UNP residues 57-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyD / Production host: Escherichia coli (E. coli) / References: UniProt: O87505, UniProt: P09986*PLUS

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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: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 80 mM Tris, 3% PGA-LM, 14% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.99998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 58658 / % possible obs: 95.3 % / Redundancy: 6 % / Net I/σ(I): 21.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.5→19.878 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 1382 3.41 %
Rwork0.2354 --
obs0.2367 40526 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 0 0 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044322
X-RAY DIFFRACTIONf_angle_d0.8315810
X-RAY DIFFRACTIONf_dihedral_angle_d15.41721
X-RAY DIFFRACTIONf_chiral_restr0.033696
X-RAY DIFFRACTIONf_plane_restr0.003740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58920.39351340.36363790X-RAY DIFFRACTION95
2.5892-2.69260.43281320.34923730X-RAY DIFFRACTION95
2.6926-2.81480.36471340.31913820X-RAY DIFFRACTION96
2.8148-2.96280.3361360.28013842X-RAY DIFFRACTION97
2.9628-3.14770.29971370.25883867X-RAY DIFFRACTION97
3.1477-3.38970.2921390.25393942X-RAY DIFFRACTION98
3.3897-3.72880.24571400.22783967X-RAY DIFFRACTION99
3.7288-4.26370.23131420.20573995X-RAY DIFFRACTION99
4.2637-5.35430.23231410.18984012X-RAY DIFFRACTION98
5.3543-19.87880.2521470.20484179X-RAY DIFFRACTION99

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