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- PDB-4ooj: Crystal structure of the N-terminal domain of the Legionella pneu... -

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Basic information

Entry
Database: PDB / ID: 4ooj
TitleCrystal structure of the N-terminal domain of the Legionella pneumophila protein SidC at 2.4A resolution
ComponentsSidC, interaptin
KeywordsUNKNOWN FUNCTION / novel fold / Legionella effector / Legionella containing vacuole / Host-Pathogen Interaction
Function / homologySidC, N-terminal / : / : / SidC N-terminal domain / SidC, C-terminal domain / SidC, lipid-binding domain / DI(HYDROXYETHYL)ETHER / SidC, interaptin
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGazdag, E.M. / Shoebel, S. / Shkumatov, A.V. / Goody, R.S. / Itzen, A.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The structure of the N-terminal domain of the Legionella protein SidC
Authors: Gazdag, E.M. / Schobel, S. / Shkumatov, A.V. / Goody, R.S. / Itzen, A.
History
DepositionFeb 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: 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 / database_2 / struct_conn / struct_ref_seq_dif / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)282,41225
Polymers280,5114
Non-polymers1,90121
Water7,548419
1
A: SidC, interaptin
B: SidC, interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,36514
Polymers140,2552
Non-polymers1,11012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-12 kcal/mol
Surface area53970 Å2
MethodPISA
2
C: SidC, interaptin
D: SidC, interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,04711
Polymers140,2552
Non-polymers7919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-26 kcal/mol
Surface area55180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.055, 119.055, 201.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
SidC, interaptin


Mass: 70127.664 Da / Num. of mol.: 4 / Fragment: UNP residues 1-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: sidC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSK6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.9558.36
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop5.60.1M sodium cacodylate, 0.2M magnesium chloride, 10% PEG 1000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop5.50.1M sodium citrate, 0.2M sodium acetate, 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9786
SYNCHROTRONSLS X10SA20.9794
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELOct 6, 2010
DECTRIS PILATUS 6M2PIXELFeb 13, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97941
ReflectionResolution: 2.4→50 Å / Num. obs: 124784 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 28.65 % / Rmerge(I) obs: 0.101 / Rsym value: 0.054 / Net I/σ(I): 19.03
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 28.32 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.87 / Rsym value: 0.473 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
PHENIX- AutoSol & PHASER - MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partial model after phasing and building in AutoSol

Resolution: 2.4→45.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.051 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 6240 5 %RANDOM
Rwork0.2 118544 --
obs0.2031 124784 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.71 Å2 / Biso mean: 50.024 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-1.11 Å20 Å2
2---2.22 Å20 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19440 0 123 419 19982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02219968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213664
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.96726992
X-RAY DIFFRACTIONr_angle_other_deg0.978333486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76452435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6325.342994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.447153540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011593
X-RAY DIFFRACTIONr_chiral_restr0.0960.22963
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023778
X-RAY DIFFRACTIONr_mcbond_it0.7881.512178
X-RAY DIFFRACTIONr_mcbond_other0.1731.54864
X-RAY DIFFRACTIONr_mcangle_it1.512219706
X-RAY DIFFRACTIONr_scbond_it2.43637790
X-RAY DIFFRACTIONr_scangle_it3.9744.57284
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 463 -
Rwork0.251 8781 -
all-9244 -
obs--100 %
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)
10.84910.1671-0.09240.331-0.08790.37270.0137-0.0191-0.1047-0.05080.0068-0.0540.03770.0567-0.02050.03370.011-0.01440.0176-0.01220.0323-34.853180.848570.9382
20.3586-0.1103-0.01450.83380.09570.42740.0333-0.0282-0.008-0.0047-0.00360.093-0.023-0.0611-0.02970.0045-0.00070.00130.03910.02060.0228-31.581878.717145.8186
30.13960.077-0.09470.3712-0.14350.2999-0.0078-0.0027-0.0792-0.04140.09190.08180.1047-0.0305-0.08410.09570.0046-0.06510.09570.02290.14695.087935.742580.8759
40.1311-0.12890.07840.4121-0.16320.3165-0.0182-0.00640.07170.04060.09660.062-0.1158-0.0385-0.07840.0902-0.01090.05430.09840.01730.13925.244733.0219103.0599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 609
2X-RAY DIFFRACTION2B2 - 609
3X-RAY DIFFRACTION3C-1 - 609
4X-RAY DIFFRACTION4D0 - 609

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