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- PDB-1jl5: Novel Molecular Architecture of YopM-a Leucine-rich Effector Prot... -

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Basic information

Entry
Database: PDB / ID: 1jl5
TitleNovel Molecular Architecture of YopM-a Leucine-rich Effector Protein from Yersinia pestis
Componentsouter protein YopM
KeywordsTOXIN / leucine-rich repeat / molecular pathogenesis / effector protein / virulence factor
Function / homology
Function and homology information


cell outer membrane / extracellular region / metal ion binding
Similarity search - Function
LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat ...LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein YopM
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEvdokimov, A.G. / Anderson, D.E. / Routzahn, K.M. / Waugh, D.S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit.
Authors: Evdokimov, A.G. / Anderson, D.E. / Routzahn, K.M. / Waugh, D.S.
History
DepositionJul 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE representing a possible biologically significant oligomerization state.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: outer protein YopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7896
Polymers51,5891
Non-polymers2005
Water6,107339
1
A: outer protein YopM
hetero molecules

A: outer protein YopM
hetero molecules

A: outer protein YopM
hetero molecules

A: outer protein YopM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,15624
Polymers206,3554
Non-polymers80220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Unit cell
Length a, b, c (Å)149.430, 149.430, 191.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

21A-300-

HOH

Detailspotentially a tetramer, same as in 1G9U

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Components

#1: Protein outer protein YopM


Mass: 51588.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YopM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P17778
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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

Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% isopropanol, 20% ethylene glycol, 0.1M MES, 0.25 M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Evdokimov, A.G., (2000) Acta Crystallog., D56, 1676.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %2-propanol1reservoir
2450 mM1reservoirCa(OAc)2
3100 mMsodium-MES1reservoir
420 %ethylene glycol1reservoir
56-8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.971 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 / Details: multilayer mirrors
RadiationMonochromator: Si crystal (X9B) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 58456 / Num. obs: 58456 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3666 / % possible all: 90.2
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 92.1 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9U

1g9u


Resolution: 2.1→70.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 137581.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2932 5 %RANDOM
Rwork0.22 ---
all0.22 58456 --
obs0.22 58456 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8124 Å2 / ksol: 0.394897 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 5 339 3137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.652.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 438 4.9 %
Rwork0.27 8575 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.27

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