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- PDB-1o5l: Crystal structure of Transcriptional regulator (TM1171) from Ther... -

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Basic information

Entry
Database: PDB / ID: 1o5l
TitleCrystal structure of Transcriptional regulator (TM1171) from Thermotoga maritima at 2.30 A resolution
Componentstranscriptional regulator, crp family
KeywordsTRANSCRIPTION / TM1171 / TRANSCRIPTIONAL REGULATOR / CRP FAMILY / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
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 / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Winged helix DNA-binding domain superfamily ...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 / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Winged helix DNA-binding domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcriptional regulator, crp family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Protein Sci. / Year: 2004
Title: On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171.
Authors: Spraggon, G. / Pantazatos, D. / Klock, H.E. / Wilson, I.A. / Woods, V.L. / Lesley, S.A.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator, crp family


Theoretical massNumber of molelcules
Total (without water)24,8951
Polymers24,8951
Non-polymers00
Water2,000111
1
A: transcriptional regulator, crp family

A: transcriptional regulator, crp family


Theoretical massNumber of molelcules
Total (without water)49,7902
Polymers49,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area3410 Å2
ΔGint-33 kcal/mol
Surface area13200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.971, 62.971, 167.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein transcriptional regulator, crp family


Mass: 24895.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1171 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0Q3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.01 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5
Details: 10% PEG-3000, 0.1M CHES pH 9.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: ammonium sulfate / Details: pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9785
DetectorType: ADSC / Detector: CCD / Date: Jun 19, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 12634 / Num. obs: 12634 / % possible obs: 100 % / Redundancy: 5.82 % / Biso Wilson estimate: 53.02 Å2 / Rsym value: 0.112 / Net I/σ(I): 22.26
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.04 % / Mean I/σ(I) obs: 1.53 / Num. unique all: 1231 / Rsym value: 0.912 / % possible all: 98.17
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 9367 / % possible obs: 99.4 % / Num. measured all: 73376 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 2.31 Å / Lowest resolution: 2.43 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.935 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. PROMINENT DENSITY NEAR RESIDUES SER64 AND ASP111 COULD BE RESIDUAL CAMP, SINCE THIS SEEMS TO BE A CAMP-BINDING CASSETTE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25324 443 4.8 %RANDOM
Rwork0.19483 ---
obs0.19743 8737 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.357 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å21.02 Å20 Å2
2--2.04 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 111 1135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221043
X-RAY DIFFRACTIONr_bond_other_d0.0010.021007
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.991408
X-RAY DIFFRACTIONr_angle_other_deg0.78232353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40725.47642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.652153
X-RAY DIFFRACTIONr_chiral_restr0.080.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_nbd_refined0.2170.2170
X-RAY DIFFRACTIONr_nbd_other0.1650.2897
X-RAY DIFFRACTIONr_nbtor_other0.0850.2596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.210
X-RAY DIFFRACTIONr_mcbond_it0.7971.5725
X-RAY DIFFRACTIONr_mcangle_it1.13721056
X-RAY DIFFRACTIONr_scbond_it1.8073428
X-RAY DIFFRACTIONr_scangle_it2.5854.5352
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 26 4.03 %
Rwork0.287 619 -
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)
15.1477-1.15750.06792.18110.78254.0282-0.0367-0.32040.4106-0.01730.080.0196-0.4471-0.1797-0.0432-0.324-0.0112-0.0084-0.1991-0.0074-0.265720.97431.2262.188
211.483-2.82831.25462.5128-0.94281.85960.22440.1901-0.28560.0121-0.12470.16750.0339-0.0061-0.0997-0.2702-0.00760.0111-0.29350.0126-0.305718.81822.674-11.174
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 9013 - 102
2291 - 129103 - 141
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.503

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