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- PDB-3cvr: Crystal structure of the full length IpaH3 -

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Basic information

Entry
Database: PDB / ID: 3cvr
TitleCrystal structure of the full length IpaH3
ComponentsInvasion plasmid antigen
KeywordsLIGASE / Leucine rich repeat and alpha fold
Function / homology
Function and homology information


: / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / extracellular region
Similarity search - Function
Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ipaH3
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhu, Y. / Shao, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structure of a Shigella effector reveals a new class of ubiquitin ligases
Authors: Zhu, Y. / Li, H. / Hu, L. / Wang, J. / Zhou, Y. / Pang, Z. / Liu, L. / Shao, F.
History
DepositionApr 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Invasion plasmid antigen


Theoretical massNumber of molelcules
Total (without water)65,5081
Polymers65,5081
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Invasion plasmid antigen

A: Invasion plasmid antigen


Theoretical massNumber of molelcules
Total (without water)131,0172
Polymers131,0172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area44060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.190, 154.190, 85.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Invasion plasmid antigen / ubiquitin E3 ligase


Mass: 65508.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 301 / Gene: ipaH_3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q83RJ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE CONFLICTS BETWEEN THE CLONED SEQUENCE IN THIS ENTRY AND THE DATABASE REFERENCE SEQUENCE. ...THERE ARE CONFLICTS BETWEEN THE CLONED SEQUENCE IN THIS ENTRY AND THE DATABASE REFERENCE SEQUENCE. THE DEPOSITOR SUGGESTS THE SEQUENCE CONFLICTS ARE NOT THE MUTATIONS BUT MAYBE THE REAL RESIDUES IN THE STAIN.

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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: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M NaCl, 0.1M Bis-Tris pH5.5, 2.5% Polyacrylic acid 5100 sodium salt, 0.1 M Sodium Nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.98
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDFeb 28, 2008
ADSC QUANTUM 2702CCDMar 3, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
211
ReflectionResolution: 2.8→51.37 Å / Num. obs: 26107 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Rmerge(I) obs: 0.071 / Rsym value: 0.074 / Net I/σ(I): 25.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.38 / % possible all: 99.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
SOLVEphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→48.76 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.888 / SU B: 25.245 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27654 1318 5.1 %RANDOM
Rwork0.25057 ---
obs0.2519 24588 99.54 %-
all-26028 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.787 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---1.44 Å20 Å2
3---2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 0 39 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223774
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9575146
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1985471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39324.607178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60115600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1781526
X-RAY DIFFRACTIONr_chiral_restr0.080.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21643
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22581
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3881.52448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63123827
X-RAY DIFFRACTIONr_scbond_it0.95231495
X-RAY DIFFRACTIONr_scangle_it1.5794.51319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 87 -
Rwork0.306 1788 -
obs--99.89 %
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)
11.6713-1.6863-1.86642.45362.00842.75840.07450.1205-0.1307-0.0294-0.00030.0655-0.031-0.0723-0.0742-0.07890.0208-0.0297-0.0381-0.10820.0189-52.9209-8.73375.6515
21.6838-1.0345-0.59390.8839-0.37152.39310.15360.12780.0548-0.3463-0.3364-0.2565-0.1773-0.01090.18280.13870.01650.2526-0.1475-0.06370.0868-14.5568-20.0934-21.0466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 268
2X-RAY DIFFRACTION2A279 - 561
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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