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- PDB-1g9u: CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERS... -

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Basic information

Entry
Database: PDB / ID: 1g9u
TitleCRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS
ComponentsOUTER PROTEIN YOPM
KeywordsTOXIN
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
ACETATE ION / : / Outer membrane protein YopM
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 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
DepositionNov 28, 2000Deposition 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: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
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)53,80520
Polymers51,5891
Non-polymers2,21619
Water4,252236
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)215,22080
Polymers206,3554
Non-polymers8,86576
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
Buried area21320 Å2
ΔGint-826 kcal/mol
Surface area57510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.359, 109.359, 101.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-3005-

HOH

21A-3030-

HOH

31A-3073-

HOH

41A-3158-

HOH

51A-3226-

HOH

DetailsPutative biological assembly is a tetramer.

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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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 10% isopropanol 0.1 M MES, 0.2-0.4 M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 321.0K
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: 0.9879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2000 / Details: synchrotron Si monochromator + Osmic mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2.32→74 Å / Num. all: 49157 / Num. obs: 39896 / % possible obs: 81 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7609 / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 74 Å

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: new structure

Resolution: 2.35→100 Å / Isotropic thermal model: isotropic per atom / Cross valid method: random 5% throughout the refinement / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2285 -random 5%
Rwork0.2 ---
all0.21 43317 --
obs0.17 33478 97 %-
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 46 236 3075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_approx_iso_adps0
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_from_restr_planes0.34
LS refinement shellResolution: 2.35→100 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.23 2285 -
Rwork0.2 --
obs-33478 77 %
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.21 / Rfactor obs: 0.17 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_planar_d0.34

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