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- PDB-3d0s: cAMP receptor protein from m.tuberculosis, cAMP-free form -

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Basic information

Entry
Database: PDB / ID: 3d0s
TitlecAMP receptor protein from m.tuberculosis, cAMP-free form
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsTRANSCRIPTION / CAMP RECEPTOR PROTEIN (CRP) / DIMER / INACTIVE(APO / UNLIGANDED) FORM / ALLOSTERY / DNA BINDING / CYCLIC AMP / TRANSCRIPTION REGULATION / CATABOLITE GENE ACTIVATOR PROTEIN / DNA-binding / Nucleotide-binding
Function / homology
Function and homology information


cell wall / cAMP binding / peptidoglycan-based cell wall / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol
Similarity search - Function
: / helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...: / helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / 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
CRP-like cAMP-activated global transcriptional regulator / CRP-like cAMP-activated global transcriptional regulator
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGallagher, D.T. / Robinson, H. / Reddy, P.T.
CitationJournal: To be Published
Title: Crystal structure of cAMP receptor protein from M. tuberculosis in the unliganded form
Authors: Gallagher, D.T. / Robinson, H. / Smith, N. / Reddy, P.T.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Mar 22, 2017Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: TRANSCRIPTIONAL REGULATORY PROTEIN
B: TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2884
Polymers50,2172
Non-polymers712
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-53 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.796, 83.803, 98.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN / CRP/FNR-FAMILY / Transcriptional regulator / Crp/Fnr family


Mass: 25108.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3777, Rv3676 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mg/mL ptn, 80 mM NaCl, l4% PEG4K, 8% IPA, 0.1M Hepes, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Nov 30, 2006
RadiationMonochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.6 % / Av σ(I) over netI: 11.6 / Number: 205215 / Rmerge(I) obs: 0.056 / Χ2: 0.94 / D res high: 2.3 Å / D res low: 30 Å / Num. obs: 17644 / % possible obs: 87.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.953099.610.0371.64413.3
3.934.9510010.0481.52213.9
3.433.9310010.0641.21814
3.123.4310010.0840.7314.4
2.93.1210010.1360.57314.4
2.732.910010.2240.49613.7
2.592.7398.410.3090.44910.1
2.482.5981.110.3660.4175.7
2.382.4854.210.3720.453.5
2.32.3839.710.4760.4212.2
ReflectionResolution: 2→30 Å / Num. obs: 29026 / % possible obs: 95.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.076.30.333193.7
2.07-2.156.50.27193.4
2.15-2.256.50.227193.3
2.25-2.376.40.188193.2
2.37-2.526.30.153192.5
2.52-2.716.30.135192.8
2.71-2.996.10.106195.7
2.99-3.4260.084199
3.42-4.360.067199.6
4.3-206.20.052198

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.56 / FOM acentric: 0.56 / FOM centric: 0.54 / Reflection: 18670 / Reflection acentric: 16221 / Reflection centric: 2449
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-27.7860.950.970.89927641286
4.1-6.60.910.940.7927192222497
3.3-4.10.840.860.733412888453
2.9-3.30.630.640.4933492952397
2.5-2.90.320.330.2358215233588
2.3-2.50.150.150.1225132285228

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.33 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28784 1448 5 %RANDOM
Rwork0.21215 ---
obs0.21585 27234 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---1.29 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 2 185 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9714703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36922.378164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88115617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7231548
X-RAY DIFFRACTIONr_chiral_restr0.1260.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022638
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21509
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22352
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.52276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58523519
X-RAY DIFFRACTIONr_scbond_it2.77931352
X-RAY DIFFRACTIONr_scangle_it4.34.51184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 107 -
Rwork0.21 1913 -
obs--92.45 %
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)
110.54783.82928.26892.02112.68039.2539-0.11920.09310.5255-0.0563-0.11760.0057-0.04030.0420.2368-0.13690.05390.0639-0.20080.0127-0.074112.2228.54924.507
22.60630.73520.25255.2712-0.3251.7301-0.0870.22140.1831-0.33080.12630.0998-0.0052-0.0676-0.0393-0.02410.0251-0.0017-0.06910.0415-0.12098.85835.3223.681
32.4112-0.0430.68680.94110.10831.1233-0.0147-0.130.00820.05210.0129-0.0173-0.0211-0.03170.0018-0.13030.0071-0.001-0.18360.0093-0.16292.80523.39636.949
45.43533.04778.73092.80395.536817.68880.1315-0.028-0.20320.0425-0.0402-0.16370.50860.0985-0.0913-0.15950.04280.0639-0.15630.0222-0.083216.56319.2326.116
50.851-1.14360.43394.49360.69341.9748-0.04130.0427-0.14490.0421-0.03570.19480.0315-0.19470.077-0.08450.0013-0.0084-0.164-0.0229-0.0707-5.3476.64821.514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B117 - 144
2X-RAY DIFFRACTION2B145 - 215
3X-RAY DIFFRACTION3A1 - 116
4X-RAY DIFFRACTION4A117 - 144
5X-RAY DIFFRACTION5A145 - 224

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