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- PDB-4a2u: CRP(CAP) from Myco. Tuberculosis, with cAMP -

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Basic information

Entry
Database: PDB / ID: 4a2u
TitleCRP(CAP) from Myco. Tuberculosis, with cAMP
ComponentsPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
KeywordsTRANSCRIPTION / CYCLIC AMP RECEPTOR / TRANSCRIPTION REGULATION / CATABOLITE GENE ACTIVATOR PROTEIN / ALLOSTERY / DNA-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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / 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: 2.63 Å
AuthorsGallagher, D.T. / Reddy, P.T.
CitationJournal: To be Published
Title: A New Crystal Form of Crp from M. Tuberculosis and Conformational Effects of Crystal Packing
Authors: Kim, S.-K. / Robinson, H. / Reddy, P.T. / Gallagher, D.T.
History
DepositionSep 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
C: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
D: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
E: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
F: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
G: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
H: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,50316
Polymers200,8698
Non-polymers2,6348
Water1,17165
1
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8764
Polymers50,2172
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-20.9 kcal/mol
Surface area20280 Å2
MethodPISA
2
C: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
D: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8764
Polymers50,2172
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-24.2 kcal/mol
Surface area20740 Å2
MethodPISA
3
E: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
F: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8764
Polymers50,2172
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-22.2 kcal/mol
Surface area20810 Å2
MethodPISA
4
G: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
H: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8764
Polymers50,2172
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-21.1 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.328, 67.801, 104.877
Angle α, β, γ (deg.)84.41, 83.46, 80.14
Int Tables number1
Space group name H-MP1
DetailsTHIS ENTRY CONTAINS FOUR DIMERS: REPRESENTED BY THE PAIRS OF CHAINS AB, CD, EF, AND GH.

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Components

#1: Protein
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/ FNR-FAMILY) / CRP / TRANSCRIPTIONAL REGULATOR\ / CRP/FNR FAMILY


Mass: 25108.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69644, UniProt: P9WMH3*PLUS
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD CHAIN LACKS RESIDUES 1-16 (DISORDER). ALL 8 CHAINS HAVE A 3-RESIDUE (SEQUENCE GSH) N-TERMINAL ...D CHAIN LACKS RESIDUES 1-16 (DISORDER). ALL 8 CHAINS HAVE A 3-RESIDUE (SEQUENCE GSH) N-TERMINAL EXPRESSION ARTIFACT. IN THE F AND H CHAINS IT IS PARTLY ORDERED.

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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: 43.3 % / Description: NONE
Crystal growpH: 5.8
Details: 8 MG PER ML PROTEIN, 25 MM CAMP, 40 MM NA CL, 10% PEG 8K, 75 MM CA ACETATE, 50 MM NA MES., pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.63→30 Å / Num. obs: 50716 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 2.63→2.75 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 64.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.63→16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.915 / SU B: 15.389 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28767 2349 5.1 %RANDOM
Rwork0.18308 ---
obs0.18853 43985 86.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.409 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-0.65 Å2-1.47 Å2
2---0.64 Å22.42 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.63→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13864 0 176 65 14105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9919295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27851770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16122.114667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.685152509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.05915207
X-RAY DIFFRACTIONr_chiral_restr0.0990.22193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 99 -
Rwork0.244 1581 -
obs--43.05 %

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