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- PDB-4pay: Crystal structure of an N-terminal fragment of the Legionella pne... -

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Entry
Database: PDB / ID: 4pay
TitleCrystal structure of an N-terminal fragment of the Legionella pneumophila effector protein SidC.
ComponentsSidC, interaptinSpace Training and Readiness Command
KeywordsTRANSPORT PROTEIN / tethering / vesicular transport / Legionella pneumophila effector
Function / homology: / : / SidC, C-terminal domain / SidC, lipid-binding domain / SidC, N-terminal / SidC N-terminal domain / : / SidC, interaptin
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.77 Å
AuthorsHorenkamp, F.A. / Mukherjee, S. / Alix, E. / Schauder, C.M. / Hubber, A.M. / Roy, C.R. / Reinisch, K.M.
CitationJournal: Traffic / Year: 2014
Title: Legionella pneumophila Subversion of Host Vesicular Transport by SidC Effector Proteins.
Authors: Horenkamp, F.A. / Mukherjee, S. / Alix, E. / Schauder, C.M. / Hubber, A.M. / Roy, C.R. / Reinisch, K.M.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJun 25, 2014ID: 4OM6
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.selection_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SidC, interaptin
B: SidC, interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,45110
Polymers140,3522
Non-polymers1,0998
Water2,990166
1
A: SidC, interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5884
Polymers70,1761
Non-polymers4123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SidC, interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8636
Polymers70,1761
Non-polymers6875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-66 kcal/mol
Surface area52120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.460, 107.584, 177.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 7 - 608 / Label seq-ID: 9 - 610

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein SidC, interaptin / Space Training and Readiness Command


Mass: 70176.023 Da / Num. of mol.: 2 / Fragment: N-terminal fragment (UNP 1-608)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: sidC, lpg2511 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZSK6
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 8% PEG 8000, 0.2M barium chloride, 0.1M Hepes, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→92.009 Å / Num. all: 52327 / Num. obs: 52258 / % possible obs: 99.8 % / Redundancy: 13 % / Net I/σ(I): 17.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.77→92.009 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 2031 3.89 %Random selection
Rwork0.1993 ---
obs0.2022 52258 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→92.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9423 0 8 166 9597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089638
X-RAY DIFFRACTIONf_angle_d0.98913063
X-RAY DIFFRACTIONf_dihedral_angle_d12.8643611
X-RAY DIFFRACTIONf_chiral_restr0.041449
X-RAY DIFFRACTIONf_plane_restr0.0061710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5400X-RAY DIFFRACTION2.758TORSIONAL
12B5400X-RAY DIFFRACTION2.758TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.8350.41721380.3113487X-RAY DIFFRACTION94
2.835-2.91160.40031450.29333520X-RAY DIFFRACTION96
2.9116-2.99730.37461380.2733562X-RAY DIFFRACTION96
2.9973-3.0940.34821470.25493534X-RAY DIFFRACTION96
3.094-3.20460.32061370.24073573X-RAY DIFFRACTION96
3.2046-3.33280.26671490.22083534X-RAY DIFFRACTION96
3.3328-3.48450.29461320.21183576X-RAY DIFFRACTION96
3.4845-3.66810.24391460.1943563X-RAY DIFFRACTION96
3.6681-3.89780.22491380.18183586X-RAY DIFFRACTION96
3.8978-4.19850.21791480.17143583X-RAY DIFFRACTION96
4.1985-4.62060.16531370.14763606X-RAY DIFFRACTION96
4.6206-5.28830.19011510.15343633X-RAY DIFFRACTION96
5.2883-6.65910.23131460.19553659X-RAY DIFFRACTION96
6.6591-44.39020.21041540.20923814X-RAY DIFFRACTION96

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