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- PDB-6bdc: Structure of Hcp1 from Flavobacterium johnsoniae -

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Basic information

Entry
Database: PDB / ID: 6bdc
TitleStructure of Hcp1 from Flavobacterium johnsoniae
ComponentsHcp1
KeywordsPROTEIN TRANSPORT / Type VI secretion / Haemolysin coregulated protein / effector chaperone
Function / homologyHemolysin coregulated protein (Hcp) TssD / Hemolysin coregulated protein Hcp (TssD) / type VI protein secretion system complex / Phage tail protein
Function and homology information
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.496 Å
AuthorsBohn, A.J. / Russell, A.B. / Robinson, H. / Mougous, J.D. / Whitney, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI080609 United States
CitationJournal: To Be Published
Title: Structure of Hcp1 from Flavobacterium johnsoniae
Authors: Bohn, A.J. / Russell, A.B. / Robinson, H. / Mougous, J.D. / Whitney, J.C.
History
DepositionOct 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hcp1


Theoretical massNumber of molelcules
Total (without water)15,8571
Polymers15,8571
Non-polymers00
Water00
1
A: Hcp1
x 6


Theoretical massNumber of molelcules
Total (without water)95,1416
Polymers95,1416
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area13590 Å2
ΔGint-84 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.021, 79.021, 82.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Hcp1


Mass: 15856.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_3262 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FET8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 21% PEG3350, 200mM sodium citrate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979, 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.0751
Reflection
Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Entry-IDDiffraction-IDNet I/σ(I)
2.7-50457798.643.16BDC141.5
2.496-501029997.846.96BDC242.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.496→41.456 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.39
RfactorNum. reflection% reflection
Rfree0.2805 980 10.02 %
Rwork0.2484 --
obs0.2519 9779 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.496→41.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 0 0 869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003892
X-RAY DIFFRACTIONf_angle_d0.7021215
X-RAY DIFFRACTIONf_dihedral_angle_d15.041517
X-RAY DIFFRACTIONf_chiral_restr0.041143
X-RAY DIFFRACTIONf_plane_restr0.003160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4957-2.62730.41441190.36661087X-RAY DIFFRACTION84
2.6273-2.79180.42451350.3571240X-RAY DIFFRACTION95
2.7918-3.00730.39481420.33881280X-RAY DIFFRACTION99
3.0073-3.30990.30631490.26871297X-RAY DIFFRACTION100
3.3099-3.78850.32361430.25841282X-RAY DIFFRACTION99
3.7885-4.7720.26211460.22231301X-RAY DIFFRACTION100
4.772-41.46220.23551460.22391312X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.7596-5.593-4.14757.48412.58877.7642-0.0749-0.1563-0.70630.9295-0.1793-0.75290.1865-0.25670.32720.7838-0.0381-0.29310.8066-0.20251.114813.857320.16421.7742
23.09252.11-3.78121.647-1.76537.66791.80220.23751.2342-2.9831-0.1085-3.7177-1.15890.4835-0.27911.07040.0870.16531.14420.16711.720121.563213.2666.4092
35.773-3.7398-1.38976.77813.37315.9438-0.2515-0.06914.73370.0592-0.25130.8262-0.33720.0278-0.60480.73460.0056-0.1320.772-0.37381.91561.913127.783721.5135
44.13150.6106-3.43017.0075-0.00278.507-0.7794-1.15963.77130.1887-0.0319-0.37670.919-0.4054-0.3640.9726-0.1082-0.2171.2051-0.44611.571613.511129.053224.2631
53.82660.49391.69445.29532.04663.1436-0.2674-0.43371.90220.27930.299-0.73280.19620.3145-0.12850.710.0301-0.14410.6641-0.15131.35537.043325.719220.4288
60.1251-0.25350.80080.5262-1.67665.2471-1.9405-0.006-0.84141.74572.502-4.03521.8274-2.38350.49411.7189-0.30580.15661.6416-0.7372.0484-5.610516.201134.0649
72.4389-1.57750.84886.60750.29335.6982-0.24360.03182.25360.2296-0.1071-1.6142-0.51830.28670.36990.7435-0.0872-0.13030.6883-0.091.601213.707924.139517.7073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 125 )

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