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- PDB-3t6k: Crystal structure of a putative response regulator (Caur_3799) fr... -

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Basic information

Entry
Database: PDB / ID: 3t6k
TitleCrystal structure of a putative response regulator (Caur_3799) from Chloroflexus aurantiacus J-10-fl at 1.86 A resolution
ComponentsResponse regulator receiver
KeywordsSIGNALING PROTEIN / Flavodoxin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


negative regulation of cell division / phosphorelay signal transduction system / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
: / AAA domain / AAA domain / 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 ...: / AAA domain / AAA domain / 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 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response regulator receiver
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical RESPONSE REGULATOR (Caur_3799) from Chloroflexus aurantiacus J-10-fl at 1.86 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Shapiro, L.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Structure summary
Revision 1.2Mar 21, 2012Group: Structure summary
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver
B: Response regulator receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,88710
Polymers30,3222
Non-polymers5658
Water6,612367
1
A: Response regulator receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6017
Polymers15,1611
Non-polymers4406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2853
Polymers15,1611
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.503, 106.503, 137.984
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21B-192-

HOH

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Components

#1: Protein Response regulator receiver


Mass: 15161.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_3799 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WCL5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 1-135) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-135) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916,0.91837,0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.918371
30.978761
ReflectionResolution: 1.86→46.117 Å / Num. obs: 39465 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.16 Å2 / Rmerge F obs: 0.145 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.15 / Net I/σ(I): 15.8 / Num. measured all: 472009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.86-1.930.8161.32.248857405540521.35899.9
1.93-20.540.9243.142698353535350.965100
2-2.090.4010.6914.146341382938280.722100
2.09-2.20.290.4995.647114388938890.521100
2.2-2.340.210.345847967398239710.3699.7
2.34-2.520.1580.2711047337391439140.283100
2.52-2.780.1080.19113.848752403740370.2100
2.78-3.180.0650.11221.947288393639360.117100
3.18-40.0360.06136.247525400540020.06399.9
40.0230.04148.648130429242840.04399.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.86→46.117 Å / Cor.coef. Fo:Fc: 0.9613 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. SULFATE AND ETHYLENE GLYCOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 1979 5.02 %RANDOM
Rwork0.1596 ---
obs0.1605 39406 --
Displacement parametersBiso max: 126.1 Å2 / Biso mean: 27.5286 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.2712 Å20 Å20 Å2
2---0.2712 Å20 Å2
3---0.5424 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 34 367 2275
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1008SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes316HARMONIC5
X-RAY DIFFRACTIONt_it2065HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2718SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2065HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2827HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2508 146 5.09 %
Rwork0.2338 2722 -
all0.2346 2868 -
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)
11.8182-1.1819-0.17091.4091-0.17360.84540.09780.13040.0283-0.1296-0.06810.0266-0.0379-0.0899-0.0297-0.03640.03270.0065-0.01630.0161-0.052123.275939.899674.707
20.5681-0.4303-0.07741.5822-0.75831.56970.0091-0.0049-0.0767-0.07960.10460.14680.129-0.1133-0.1137-0.0279-0.0129-0.014-0.03660.0189-0.017239.598623.007463.5328

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