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- PDB-4ev0: Crystal Structure of Thermus thermophilus Catabolite Activator Protein -

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Basic information

Entry
Database: PDB / ID: 4ev0
TitleCrystal Structure of Thermus thermophilus Catabolite Activator Protein
ComponentsTranscription regulator, Crp familyTranscriptional regulation
KeywordsTRANSCRIPTION ACTIVATOR / cAMP binding / winged helix-turn-helix motif / DNA binding
Function / homology
Function and homology information


cAMP binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of gene expression / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic AMP receptor protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.402 Å
AuthorsHudson, B.P. / Turo, K. / Birktoft, J.J. / Lawson, C.L.
CitationJournal: To be Published
Title: Crystal Structure of T. thermophilius Catabolite Activator Protein
Authors: Hudson, B.P. / Turo, K. / Birktoft, J.J. / Ebright, R.H. / Lawson, C.L.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transcription regulator, Crp family
D: Transcription regulator, Crp family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86010
Polymers47,6972
Non-polymers1,1638
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-104 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.250, 94.842, 121.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13A
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resseq 5:55 or resseq 64:108) and (name...A5 - 55
121(chain 'A' and (resseq 5:55 or resseq 64:108) and (name...A64 - 108
211(chain 'D' and (resseq 5:55 or resseq 64:108) and (name...D5 - 55
221(chain 'D' and (resseq 5:55 or resseq 64:108) and (name...D64 - 108
112chain 'A' and (resseq 112:133) and (name n or name ca or name c or name o)A0
212chain 'D' and (resseq 112:133) and (name n or name ca or name c or name o)D0
113chain 'A' and (resseq 140:153 or resseq 160:216) and (name n or name ca or name c or name o)A140 - 153
123chain 'A' and (resseq 140:153 or resseq 160:216) and (name n or name ca or name c or name o)A160 - 216
213chain 'D' and (resseq 140:153 or resseq 160:216) and (name n or name ca or name c or name o)D140 - 153
223chain 'D' and (resseq 140:153 or resseq 160:216) and (name n or name ca or name c or name o)D160 - 216

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.571066, 0.627406, -0.529382), (0.625286, -0.08538, -0.775711), (-0.531884, -0.773998, -0.34355)54.893902, 73.396004, 132.065002
2given(-0.642087, 0.541131, -0.543048), (0.587761, -0.10731, -0.801886), (-0.4922, -0.834063, -0.249153)64.318802, 78.229103, 128.931
3given(-0.71789, 0.682395, -0.137735), (0.66787, 0.619282, -0.412844), (-0.196426, -0.388365, -0.900327)44.236698, 25.666, 154.419998

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Components

#1: Protein Transcription regulator, Crp family / Transcriptional regulation


Mass: 23848.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RIKEN BIOResource Center, plasmid TTHA1437 of single clone (RDB 6078)
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: crp, TTHA1437 / Plasmid: pET-ttCRP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SID7
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Screening for crystallization used the Gryphon liquid handling system (Art Robbins Instruments). Crystals were grown using sitting drops (200 nL protein + 200 nL crystallization reagent) ...Details: Screening for crystallization used the Gryphon liquid handling system (Art Robbins Instruments). Crystals were grown using sitting drops (200 nL protein + 200 nL crystallization reagent) with 60 UL reservoirs of crystallization reagent in a 96-well high-throughput screen. Plate-shaped crystals were obtained at 20 degree C using Hampton Research NATRIX HT #38: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 5% (w/v) polyethylene glycol 4000, and 0.05 M HEPES sodium, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2010
RadiationMonochromator: double crystal monochromator with vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 20242 / Num. obs: 20242 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.08 / Χ2: 2.318 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.446.50.5655350.804150.6
2.44-2.496.60.4816240.831161.1
2.49-2.53120.3968480.966179
2.53-2.5915.30.3999370.955187.9
2.59-2.6416.90.36510280.962196.7
2.64-2.719.10.35410631.012199.6
2.7-2.7724.10.28910431.0661100
2.77-2.8528.80.26510591.0841100
2.85-2.9328.80.2310661.1741100
2.93-3.0229.10.18710591.2771100
3.02-3.13290.16110671.441100
3.13-3.2629.10.13510731.6691100
3.26-3.4128.90.10910732.0791100
3.41-3.5928.90.09710852.5171100
3.59-3.8128.80.08610803.0711100
3.81-4.128.60.07410733.5631100
4.1-4.5228.30.06710974.0971100
4.52-5.17280.06811074.2731100
5.17-6.5127.20.07211234.031100
6.51-10025.20.04512023.857199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw

2pqq

3d0s

3h3u

2zcw


Resolution: 2.402→44.173 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7767 / SU ML: 0.36 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
Details: Disorder modelled using 6 TLS groups, 3 per subunit
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1031 5.11 %5% randomly selected
Rwork0.2 ---
obs0.2028 20187 93.67 %-
all-20242 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.5 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 159.29 Å2 / Biso mean: 64.9012 Å2 / Biso min: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-28.9091 Å2-0 Å2-0 Å2
2---15.1925 Å20 Å2
3----13.7167 Å2
Refinement stepCycle: LAST / Resolution: 2.402→44.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 70 82 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083463
X-RAY DIFFRACTIONf_angle_d1.1654700
X-RAY DIFFRACTIONf_chiral_restr0.073535
X-RAY DIFFRACTIONf_plane_restr0.004605
X-RAY DIFFRACTIONf_dihedral_angle_d18.0711292
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A384X-RAY DIFFRACTIONPOSITIONAL0.297
12D384X-RAY DIFFRACTIONPOSITIONAL0.297
21A88X-RAY DIFFRACTIONPOSITIONAL0.318
22D88X-RAY DIFFRACTIONPOSITIONAL0.318
31A284X-RAY DIFFRACTIONPOSITIONAL0.346
32D284X-RAY DIFFRACTIONPOSITIONAL0.346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4021-2.52870.39261050.26691756186162
2.5287-2.68720.34261480.25562664281293
2.6872-2.89460.28221650.240628883053100
2.8946-3.18580.28471430.219328853028100
3.1858-3.64660.25981470.213429373084100
3.6466-4.59360.20411440.17429593103100
4.5936-44.18010.24921790.186630673246100
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)
11.24191.0836-0.79322.023-1.36865.0065-0.05280.2318-0.3095-0.24070.22570.0187-0.0363-0.3722-0.00010.2872-0.0139-0.01030.47580.03950.500237.359443.870540.4098
20.32890.0166-0.05460.5509-0.61851.1978-0.01130.3563-0.01110.20270.17-0.2505-0.3054-0.77260.00010.866-0.07440.02910.4676-0.02070.513535.865454.45450.3507
33.12151.0659-0.53723.7313-0.58672.2406-0.05930.01680.10820.15230.04590.0702-0.1081-0.31290.00010.30620.05130.01550.5114-0.01710.443719.682832.056378.0315
41.93510.8221-0.33441.43020.38491.857-0.0291-0.13520.1134-0.13370.0566-0.0048-0.4134-0.06880.00010.8713-0.00880.00910.3669-0.00340.460240.367362.455163.7744
52.07390.4042-1.14611.2308-0.86580.9933-0.2041-0.0722-0.68990.0324-0.3664-0.316-0.3025-0.0623-0.05150.934-0.1632-0.02570.4456-0.00280.488442.907352.01654.438
62.029-0.408-0.72071.13561.4152.302-0.2287-0.11650.21210.31930.3124-0.36090.57080.31690.02470.33230.06620.09770.477-0.00590.506836.770116.900569.3375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:109 OR RESID 301:301 ) )A4 - 109
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:109 OR RESID 301:301 ) )A301
3X-RAY DIFFRACTION2( CHAIN A AND RESID 110:135 )A110 - 135
4X-RAY DIFFRACTION3( CHAIN A AND RESID 136:216 )A136 - 216
5X-RAY DIFFRACTION4( CHAIN D AND ( RESID 3:109 OR RESID 301:301 ) )D3 - 109
6X-RAY DIFFRACTION4( CHAIN D AND ( RESID 3:109 OR RESID 301:301 ) )D301
7X-RAY DIFFRACTION5( CHAIN D AND RESID 110:135 )D110 - 135
8X-RAY DIFFRACTION6( CHAIN D AND RESID 136:216 )D136 - 216

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