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- PDB-3lyq: Crystal structure of IpgB2 from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 3lyq
TitleCrystal structure of IpgB2 from Shigella flexneri
ComponentsIpgB2
KeywordsRHOA-BINDING PROTEIN / IpgB2 / GEF / WxxxE / TTSS effector protein / bacterial GEF / cytoskeleton dynamics
Function / homologySopE-like GEF fold - #20 / Bacterial effector protein IpgB-like / IpaB/EvcA family / SopE-like GEF fold / Orthogonal Bundle / Mainly Alpha / MU-OXO-DIIRON / CITRATE ANION / IpgB2
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKlink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of Shigella IPGB2 in complex with human RhoA: Implications for the mechanism of bacterial GEF-mimicry
Authors: Klink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: IpgB2
B: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6957
Polymers43,8722
Non-polymers8235
Water1,910106
1
A: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3804
Polymers21,9361
Non-polymers4443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3143
Polymers21,9361
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.080, 114.080, 88.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL UNITS, WHICH INTERACT VIA DOMAIN-SWAPPING.

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Components

#1: Protein IpgB2 / IpgB2 / probably secreted by the Mxi-Spa secretion machinery


Mass: 21935.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgB2 / Plasmid: pET-M 41 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9AJW7
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 5% (w/w) PEG 3350, 7% isopropanol, 10mM FeCl3, 100mM trisodium citrate/citric acid pH 5.5, 10mM NaCl, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.9
SYNCHROTRONESRF ID23-120.979
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 21, 2008
MARRESEARCH2CCDNov 25, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.9791
ReflectionRedundancy: 11.8 % / Av σ(I) over netI: 7.4 / Number: 186094 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / D res high: 2.8 Å / D res low: 90.909 Å / Num. obs: 15757 / % possible obs: 99.3
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
8.8548.97323770.0510.0518.6
6.268.8559799.90.050.0510.9
5.116.267451000.0590.05911.5
4.435.118701000.050.0511.7
3.964.439681000.0540.05411.9
3.613.9610661000.0720.07212
3.353.6111511000.1050.10512
3.133.3512231000.1870.18712.1
2.953.1313081000.4150.41512.1
2.82.9513671000.8250.82512.2
ReflectionResolution: 2.3→22.88 Å / Num. obs: 25363 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.35
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 7703 / Num. unique all: 1205 / Num. unique obs: 1205 / % possible all: 63

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
DMphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→22.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.362 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.281 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY; An almost spherical complex of ligands mediates a strong crystallographic contact between four different IpgB2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY; An almost spherical complex of ligands mediates a strong crystallographic contact between four different IpgB2 molecules. The cluster contains at least two iron atoms with a Fe-Fe-distance identical to the distance in MU-OXO-DIIRON. An interpretation as a Fe-citrate cluster containing four citrate molecules lowers both free and working R factor significantly. However, the precise architecture of the cluster used for this interpretation (chain A or B) only represents the "best compromise". Ligands in chain A or B may not be completely correct, contain unrealistic atom distances and do not perfectly describe the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1267 5 %RANDOM
Rwork0.229 ---
obs0.232 24089 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.13 Å2 / Biso mean: 45.838 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 45 106 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223044
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9594075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74225.034145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36315607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8531518
X-RAY DIFFRACTIONr_chiral_restr0.1640.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022234
X-RAY DIFFRACTIONr_mcbond_it0.8251.51842
X-RAY DIFFRACTIONr_mcangle_it1.57622989
X-RAY DIFFRACTIONr_scbond_it2.24931202
X-RAY DIFFRACTIONr_scangle_it3.8254.51086
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 59 -
Rwork0.31 1137 -
all-1196 -
obs--63.18 %
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)
11.41770.05590.15070.57860.09550.18890.0641-0.15990.11880.1518-0.00650.1420.0063-0.1396-0.05760.225-0.0392-0.02370.1620.0430.287139.695-14.50910.111
23.1222-1.0291-0.18672.167-2.5468.8205-0.3821-0.7701-0.6169-0.046-0.1621-0.28650.54730.57690.54420.34710.0922-0.08350.37410.23610.439940.287-23.65135.611
31.8606-0.0278-1.49142.10.50692.8367-0.0574-0.617-0.11740.5338-0.12370.04350.05650.34090.18110.1851-0.0348-0.01790.24670.07830.354134.913-17.1920.949
41.2441-0.797-0.2831.34160.26170.8780.06810.1149-0.11290.0225-0.0315-0.11330.15550.0891-0.03670.1612-0.0519-0.03320.23940.04140.344850.546-22.773-6.108
53.20960.74330.27341.9523-1.16048.67310.2867-0.06870.3147-0.5986-0.21780.8566-0.3609-0.6172-0.06890.37260.1716-0.29090.2586-0.07320.46142.588-26.589-32.417
61.7138-0.2147-1.24452.13741.23613.0570.09390.5312-0.0091-0.4319-0.13720.1321-0.2419-0.16620.04340.13310.0265-0.06160.22450.04040.314850.6-28.322-17.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 76
2X-RAY DIFFRACTION2A77 - 110
3X-RAY DIFFRACTION3A111 - 185
4X-RAY DIFFRACTION4B2 - 76
5X-RAY DIFFRACTION5B77 - 111
6X-RAY DIFFRACTION6B112 - 185

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