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- PDB-3tmy: CHEY FROM THERMOTOGA MARITIMA (MN-III) -

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Basic information

Entry
Database: PDB / ID: 3tmy
TitleCHEY FROM THERMOTOGA MARITIMA (MN-III)
ComponentsCHEY PROTEIN
KeywordsCHEMOTAXIS / PHOSPHORYL TRANSFER / SIGNAL TRANSDUCTION / MANGANESE BINDING
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chemotaxis protein CheY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUsher, K.C. / De La Cruz, A. / Dahlquist, F.W. / Remington, S.J.
Citation
Journal: Protein Sci. / Year: 1998
Title: Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability.
Authors: Usher, K.C. / de la Cruz, A.F. / Dahlquist, F.W. / Swanson, R.V. / Simon, M.I. / Remington, S.J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Magnesium Binding to the Bacterial Chemotaxis Protein Chey Results in Large Conformational Changes Involving its Functional Surface
Authors: Bellsolell, L. / Prieto, J. / Serrano, L. / Coll, M.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-A Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionJun 4, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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: CHEY PROTEIN
B: CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5794
Polymers26,4702
Non-polymers1102
Water68538
1
A: CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2902
Polymers13,2351
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2902
Polymers13,2351
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.658, 64.719, 33.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.940939, 0.168462, -0.293692), (0.076435, -0.950728, -0.300455), (-0.329836, 0.260261, -0.907453)
Vector: -10.07741, 55.72342, 6.31763)

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Components

#1: Protein CHEY PROTEIN / TMY


Mass: 13234.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location: CYTOPLASM / Gene: CHEY / Plasmid: PQE12 / Cellular location (production host): CYTOPLASM / Gene (production host): CHEY / Production host: Escherichia coli (E. coli) / Strain (production host): K0641/RECA / References: UniProt: Q56312
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.3 Å3/Da / Density % sol: 51 %
Crystal growpH: 7
Details: 0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MANGANESE CHLORIDE
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
215 mMmagnesium chloride1reservoir
30.2 Mammonium sulfate1reservoir
40.1 MHEPES1reservoir
525 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 15, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 12436 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 2.5 / % possible all: 94
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
SDMS(DCREDUCE)data reduction
SDMS(SCALE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TMY

1tmy


Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: DISORDERED SIDE-CHAINS WERE MODELED STEREOCHEMICALLY AND HAVE THEIR OCCUPANCY SET ARBITRARILY TO 0.0.
RfactorNum. reflection% reflection
Rwork0.182 --
all-12436 -
obs-12436 97 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 576 Å2 / ksol: 1.03 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 2 38 1840
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01618261.5
X-RAY DIFFRACTIONt_angle_deg2.4424383
X-RAY DIFFRACTIONt_dihedral_angle_d19.411500
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018482
X-RAY DIFFRACTIONt_gen_planes0.0212545
X-RAY DIFFRACTIONt_it7.918261
X-RAY DIFFRACTIONt_nbd0.0272420
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.021 / Weight: 5

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