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- PDB-6db1: 2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Bi... -

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Basic information

Entry
Database: PDB / ID: 6db1
Title2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica
ComponentsPutative methyl-accepting chemotaxis protein
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Chemotaxis
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). ...Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyl-accepting chemotaxis protein
B: Putative methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7013
Polymers35,6662
Non-polymers351
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-15 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.226, 89.226, 65.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-310-

HOH

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Components

#1: Protein Putative methyl-accepting chemotaxis protein


Mass: 17832.814 Da / Num. of mol.: 2 / Fragment: residues 34-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM3152 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8ZM14
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein: 7.0 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg, Screen: PACT (C5), 0.1 PCB buffer (pH 8.0), 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20259 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Rsym value: 0.075 / Χ2: 1.861 / Net I/σ(I): 28.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1009 / CC1/2: 0.718 / Rpim(I) all: 0.415 / Rrim(I) all: 0.926 / Rsym value: 0.826 / Χ2: 1.006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.137 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26448 1036 5.1 %RANDOM
Rwork0.22218 ---
obs0.22438 19193 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.644 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0.91 Å20 Å2
2---1.82 Å20 Å2
3---5.91 Å2
Refinement stepCycle: 1 / Resolution: 2→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 1 81 2191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0152252
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181977
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.8053052
X-RAY DIFFRACTIONr_angle_other_deg0.4761.8364672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2115292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.18520.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9931523
X-RAY DIFFRACTIONr_chiral_restr0.0660.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0212629
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1123.1951141
X-RAY DIFFRACTIONr_mcbond_other2.1113.1961142
X-RAY DIFFRACTIONr_mcangle_it3.2524.7581442
X-RAY DIFFRACTIONr_mcangle_other3.2524.761443
X-RAY DIFFRACTIONr_scbond_it2.5363.4321110
X-RAY DIFFRACTIONr_scbond_other2.5233.4291109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9635.0871611
X-RAY DIFFRACTIONr_long_range_B_refined6.68240.5242626
X-RAY DIFFRACTIONr_long_range_B_other6.67840.4052617
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 74 -
Rwork0.34 1418 -
obs--99.93 %
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)
13.57650.7621-1.49019.5617-3.18922.6055-0.47670.2369-0.466-0.04660.3323-0.44580.0627-0.09630.14440.20950.02490.02090.1065-0.07940.118535.64682.54230.6594
23.294.6719-0.18259.14923.12844.7606-0.18260.3509-0.50070.08260.1115-0.97320.5723-0.52890.0710.35850.02710.07190.13650.00820.927835.0855-20.66017.5389
36.4545-2.79740.94157.3922-1.74813.6273-0.2917-0.27950.00530.55450.4388-0.1275-0.1035-0.2337-0.14710.25970.0971-0.02620.1551-0.02940.019229.35126.33686.2934
41.80873.9377-0.94548.669-2.43752.4881-0.02760.0617-0.1778-0.0060.241-0.29710.0924-0.3436-0.21350.26350.05390.07710.2070.09090.149924.6371-10.76818.7984
50.41081.87471.436510.00027.63165.8571-0.0615-0.0627-0.0139-1.1703-0.0293-0.0079-0.8514-0.04540.09080.5549-0.13030.06390.12420.03410.319521.153-17.56993.8063
61.15313.1011-2.169912.572-4.87254.5058-0.15380.24070.0078-0.38610.2066-0.09230.1239-0.5219-0.05280.1922-0.0121-0.03510.19380.00330.04126.20826.7576-6.1276
79.09167.01710.43628.06741.06621.9953-0.05090.31190.1219-0.01080.0783-0.1468-0.05260.0123-0.02740.15910.0003-0.04920.1695-0.10170.134444.424413.1846-7.2182
86.55393.0439-0.07935.48530.79513.8212-0.09430.4539-0.6047-0.2338-0.01610.12690.4522-0.59870.11040.3522-0.1104-0.03130.3797-0.19340.166328.2136-5.546-15.4505
92.12022.6449-1.32926.3466-1.38681.438-0.29430.3031-0.2951-0.29380.1081-0.52180.01320.04050.18620.2116-0.03520.01350.2906-0.13350.2849.49788.6127-12.6829
1011.92216.74235.71695.05964.16574.013-0.14450.3258-0.0975-0.17350.1984-0.26840.15270.1184-0.05380.2093-0.01220.0460.1383-0.08450.141942.8255-5.0849-16.2606
116.20933.88761.77478.86072.01989.56020.2607-0.2765-0.83680.5614-0.4344-0.01890.4028-0.58570.17370.143-0.1103-0.00360.09460.00580.166633.0668-17.8472-14.6948
121.42662.25923.62057.91045.56159.21150.4362-0.20910.02230.9824-0.5423-0.73521.054-0.55240.10610.1781-0.0367-0.06450.1251-0.03790.252944.9495-5.0198-6.0306
137.15516.35010.96927.48590.58175.65350.2323-0.203-0.27820.5695-0.1994-0.60650.1084-0.0129-0.03290.1239-0.0243-0.10820.07280.02350.137150.812212.5422.3656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 68
2X-RAY DIFFRACTION2A69 - 91
3X-RAY DIFFRACTION3A92 - 117
4X-RAY DIFFRACTION4A118 - 142
5X-RAY DIFFRACTION5A143 - 152
6X-RAY DIFFRACTION6A153 - 179
7X-RAY DIFFRACTION7B42 - 61
8X-RAY DIFFRACTION8B62 - 95
9X-RAY DIFFRACTION9B96 - 113
10X-RAY DIFFRACTION10B114 - 138
11X-RAY DIFFRACTION11B139 - 149
12X-RAY DIFFRACTION12B150 - 166
13X-RAY DIFFRACTION13B167 - 176

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