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- PDB-4fmt: Crystal structure of a ChpT protein (CC_3470) from Caulobacter cr... -

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Entry
Database: PDB / ID: 4fmt
TitleCrystal structure of a ChpT protein (CC_3470) from Caulobacter crescentus CB15 at 2.30 A resolution
ComponentsChpT protein
KeywordsTRANSFERASE / a phosphotransfer protein / a two-component signaling pathway / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Histidine phosphotransferase ChpT, C-terminal / Histidine phosphotransferase C-terminal domain / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histidine phosphotransferase ChpT C-terminal domain-containing protein
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Shapiro, L.
CitationJournal: Structure / Year: 2013
Title: Branched signal wiring of an essential bacterial cell-cycle phosphotransfer protein.
Authors: Blair, J.A. / Xu, Q. / Childers, W.S. / Mathews, I.I. / Kern, J.W. / Eckart, M. / Deacon, A.M. / Shapiro, L.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ChpT protein
B: ChpT protein
C: ChpT protein
D: ChpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,14312
Polymers94,6834
Non-polymers4608
Water5,603311
1
A: ChpT protein
B: ChpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5726
Polymers47,3412
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-64 kcal/mol
Surface area18670 Å2
MethodPISA
2
C: ChpT protein
D: ChpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5726
Polymers47,3412
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-62 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.190, 94.320, 100.610
Angle α, β, γ (deg.)90.000, 92.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ChpT protein


Mass: 23670.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: CC_3470 / Plasmid: pET-28b(+) / Production host: Escherichia Coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9A2T6
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSSHHHHHHSSGLVPRGSH. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSSHHHHHHSSGLVPRGSH. THE TAG WAS REMOVED WITH THROMBIN LEAVING ONLY (-2)-GLY-SER-HIS-(0) FOLLOWED BY THE FULL LENGTH TARGET SEQUENCE (1-225). THE START CODON FOR UNIPROT ENTRY A6H916 WAS MIS-ANNOTATED (SEE PMID 21878915). THE CLONED CONSTRUCT STARTS FROM THE CORRECT START CODON THAT CORRESPONDS TO MET-29 OF UNIPROT ENTRY A6H916 (VERSION 1 OF THE SEQUENCE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.2662.32THE STRUCTURE WAS SOLVED USING TWO WAVELENGTH MAD PHASES FROM A HEAVY ATOM (GOLD) DERIVATIVE OF ANOTHER CRYSTAL. THE PHASING CRYSTAL DIFFRACTED TO 2.95 A. TO OBTAIN HEAVY ATOM DERIVATIVES, CRYSTALS WERE SOAKED IN CRYO SOLUTION CONTAINING 0.01 M POTASSIUM DICYANOAURATE FOR 190 MINUTES. THE STRUCTURE WAS REFINED AT 2.3 A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
295.51vapor diffusion, hanging drop6.220% (w/v) PEG-8000, 0.1M MES pH 6.0, 0.2M Calcium acetate, final pH 6.2, VAPOR DIFFUSION,HANGING DROP, temperature 295.5K
295.52vapor diffusion, hanging drop6.220% (w/v) PEG-8000, 0.1M MES pH 6.0, 0.2M Calcium acetate, final pH 6.2, VAPOR DIFFUSION,HANGING DROP, temperature 295.5K
Experiment crystal cryo treatment
Crystal-IDCooling detailsFinal solution detailsSoaking details
1Direct immersion in liquid nitrogen30% (w/v) PEG-8000 in precipitant
2Direct immersion in liquid nitrogen30% (w/v) PEG-8000, 0.01 M potassium dicyanoaurate (I) in precipitantFirst the PEG-8000 was increased to 30% (w/v) PEG-8000 in precipitant. Potassium dicyanoaurate (I) was then added to a final concentration of 0.010 M and after 190 minutes the crystal was harvested.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL12-220.8731,1.0395
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELJul 15, 2011Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
DECTRIS PILATUS 6M2PIXELJul 25, 2011Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.87311
31.03951
ReflectionResolution: 2.3→65.094 Å / Num. obs: 52631 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 51.445 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.67
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.363.430.9121.6413267386997.6
2.36-2.423.40.77212793377197
2.42-2.493.30.6972.211667357994.3
2.49-2.573.50.4843.412491357098
2.57-2.663.60.4054.412906355499.4
2.66-2.753.60.315.412385343199.4
2.75-2.853.60.2696.111980332199.2
2.85-2.973.60.1987.811331316699.2
2.97-3.13.50.1619.210632304098.7
3.1-3.253.30.12310.78996275594.4
3.25-3.433.60.08714.59843275998
3.43-3.643.50.06817.59066257297.7
3.64-3.893.40.05719.38264240396.7
3.89-4.23.40.0520.97602225296.6
4.2-4.63.20.04223.66539202394.4
4.6-5.143.30.038245801178492.5
5.14-5.943.50.04123.55913169797.9
5.94-7.273.40.03624.24825141196.5
7.27-10.293.10.02727.73341106694.9
10.29-65.093.50.02930.7212160794.1

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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-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→65.094 Å / Cor.coef. Fo:Fc: 0.9408 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT EXCEPT FOR ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT EXCEPT FOR THE FINAL REFINEMENT CYCLE. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. NA IONS AND GLYCEROL MODELED ARE PRESENT IN PURIFICATION/CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2682 5.1 %RANDOM
Rwork0.1838 ---
obs0.1853 52619 97.16 %-
Displacement parametersBiso max: 197.23 Å2 / Biso mean: 54.2108 Å2 / Biso min: 26.03 Å2
Baniso -1Baniso -2Baniso -3
1--8.3126 Å20 Å25.188 Å2
2---0.1905 Å20 Å2
3---8.5031 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.3→65.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 28 311 6391
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2899SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes960HARMONIC5
X-RAY DIFFRACTIONt_it6257HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion832SEMIHARMONIC5
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_contact7229SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6257HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8517HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion2.57
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2687 199 5.16 %
Rwork0.2488 3659 -
all0.2498 3858 -
obs--97.16 %
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)
11.3874-1.5128-0.19091.609-0.42562.44740.0031-0.16370.0108-0.13770.09890.0743-0.10110.0807-0.1019-0.0429-0.02140.0066-0.12640.0141-0.12624.278154.07313.6465
21.2768-0.92510.30741.34890.04411.9896-0.0762-0.1588-0.0597-0.14070.03010.090.084-0.0880.046-0.0103-0.01460.0141-0.10820.012-0.132143.223535.154212.6547
31.805-0.03450.77881.58671.37012.33420.09730.0820.07650.06630.037-0.00050.15690.1559-0.1343-0.0679-0.0354-0.0074-0.11630.0176-0.13114.194177.554465.4538
41.664-0.95030.30392.05661.56121.5056-0.0938-0.20960.03840.20710.1878-0.12660.13530.2818-0.0939-0.1055-0.0166-0.0053-0.03190.0017-0.137914.23158.383349.1902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|17 - 225 }A17 - 225
2X-RAY DIFFRACTION2{ B|18 - 225 }B18 - 225
3X-RAY DIFFRACTION3{ C|18 - 225 }C18 - 225
4X-RAY DIFFRACTION4{ D|18 - 225 }D18 - 225

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