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- PDB-6ceq: The Aer2 Receptor from Vibrio cholerae is a Dual PAS-Heme Oxygen ... -

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Basic information

Entry
Database: PDB / ID: 6ceq
TitleThe Aer2 Receptor from Vibrio cholerae is a Dual PAS-Heme Oxygen Sensor
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / PAS domain / Vibrio cholera / chemoreceptor / heme / signal transduction
Function / homology
Function and homology information


plasma membrane => GO:0005886 / transmembrane signaling receptor activity / chemotaxis / signaling receptor activity / signal transduction
Similarity search - Function
HAMP domain / PAS domain / 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 (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...HAMP domain / PAS domain / 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 (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / PAS domain
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsCrane, B.R. / Chua, T.K. / Sukomon, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122535 United States
CitationJournal: Mol. Microbiol. / Year: 2018
Title: THE AER2 RECEPTOR FROM VIBRIO CHOLERAE IS A DUAL PAS-HEME OXYGEN SENSOR.
Authors: Greer-Phillips, S.E. / Sukomon, N. / Chua, T.K. / Johnson, M.S. / Crane, B.R. / Watts, K.J.
History
DepositionFeb 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8136
Polymers36,9643
Non-polymers1,8493
Water5,693316
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9382
Polymers12,3211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9382
Polymers12,3211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9382
Polymers12,3211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.512, 62.512, 157.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-554-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 12321.304 Da / Num. of mol.: 3 / Fragment: PAS 2 domain (UNP residues 170-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CSW01_19535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2BEZ7, UniProt: Q9KKL2*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.6 M ammonium sulfate, 0.1 M citric acid, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6279 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6279 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 47018 / % possible obs: 96.7 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.049 / Rrim(I) all: 0.144 / Χ2: 2.592 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.59-1.6221.61713450.1961.1842.0180.72456.6
1.62-1.652.62.43719570.1461.5862.9310.62282
1.65-1.683.72.33522850.1761.3052.6910.67196.2
1.68-1.715.22.10523790.3160.9952.3360.66799.3
1.71-1.756.72.32223970.3920.9642.5180.68100
1.75-1.797.91.97424180.5510.752.1140.69100
1.79-1.848.51.79824200.6070.6581.9170.747100
1.84-1.898.81.29123690.7060.4631.3740.77100
1.89-1.949.10.94924400.7950.3321.0070.764100
1.94-29.20.53424140.9110.1850.5660.805100
2-2.079.30.43223870.940.1490.4580.901100
2.07-2.169.30.36524270.9640.1260.3860.92100
2.16-2.269.30.28824260.9740.10.3050.985100
2.26-2.389.30.23324120.9810.0810.2471.155100
2.38-2.529.30.18624300.9870.0640.1971.215100
2.52-2.729.20.14624590.9910.0510.1551.40899.8
2.72-2.999.20.10424480.9920.0360.1111.99899.8
2.99-3.439.10.07924620.9960.0280.0843.2199.7
3.43-4.3290.06325060.9970.0220.0675.08899.6
4.32-508.50.06326370.9910.0230.06821.1498.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.67→27.165 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1795 4.27 %
Rwork0.2032 --
obs0.2046 42063 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→27.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 316 3014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072767
X-RAY DIFFRACTIONf_angle_d1.123789
X-RAY DIFFRACTIONf_dihedral_angle_d8.5661634
X-RAY DIFFRACTIONf_chiral_restr0.055414
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.71510.37581340.33773011X-RAY DIFFRACTION98
1.7151-1.76560.37551390.31323042X-RAY DIFFRACTION100
1.7656-1.82260.32771340.30423070X-RAY DIFFRACTION100
1.8226-1.88770.30161370.26893069X-RAY DIFFRACTION100
1.8877-1.96330.27651390.23833069X-RAY DIFFRACTION100
1.9633-2.05260.25981310.22113049X-RAY DIFFRACTION100
2.0526-2.16080.26991410.21243097X-RAY DIFFRACTION100
2.1608-2.29610.24911330.20463073X-RAY DIFFRACTION100
2.2961-2.47330.26091380.20693114X-RAY DIFFRACTION100
2.4733-2.72190.2271420.21633115X-RAY DIFFRACTION100
2.7219-3.11530.27121390.20063120X-RAY DIFFRACTION100
3.1153-3.92310.18671390.17463183X-RAY DIFFRACTION100
3.9231-27.16850.1921490.17233256X-RAY DIFFRACTION98

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