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- PDB-1hw5: THE CAP/CRP VARIANT T127L/S128A -

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Basic information

Entry
Database: PDB / ID: 1hw5
TitleTHE CAP/CRP VARIANT T127L/S128A
ComponentsCATABOLITE GENE ACTIVATOR
KeywordsGENE REGULATION / cAMP Receptor Protein / Catabolite Activator Protein (CAP) Transcription / Allostery / cAMP / cyclic AMP Mutant
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / 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 / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsChu, S.Y. / Tordova, M. / Gilliland, G.L. / Gorshkova, I. / Shi, Y.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The structure of the T127L/S128A mutant of cAMP receptor protein facilitates promoter site binding
Authors: Chu, S.Y. / Tordova, M. / Gilliland, G.L. / Gorshkova, I. / Shi, Y. / Wang, S. / Schwarz, F.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The Structure of a CAP-DNA Complex Having Two cAMP Molecules Bound To Each Monomer
Authors: Passner, J.M. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of a Complex of Catabolite Gene Activator Protein and Cyclic AMP Refined at 2.5 A Resolution
Authors: Weber, I.T. / Steitz, T.A.
#3: Journal: J.Biol.Chem. / Year: 1987
Title: Crystal Structure of a Cyclic AMP-independent Mutant of Catabolite Gene Activator Protein
Authors: Weber, I.T. / Gilliland, G.L. / Harman, J.G. / Peterkofsky, A.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATABOLITE GENE ACTIVATOR
B: CATABOLITE GENE ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3255
Polymers47,3372
Non-polymers9883
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-39 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.1, 93.1, 104.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe dimer in the asymmetric unit is the biological unit

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Components

#1: Protein CATABOLITE GENE ACTIVATOR / CAMP RECEPTOR PROTEIN


Mass: 23668.494 Da / Num. of mol.: 2 / Mutation: T127L, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CRP/CAP / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P0ACJ8
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 4K, isoprotanol, cAMP, HEPES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.8 mg/mlprotein1drop
210 mMTris-HCl1drop
30.2 mMEDTA1drop
45 %(v/v)glycerol1drop
50.5 M1dropKCl
60.2 mMdithiothreitol1drop
710 %(w/v)PEG40001reservoir
87 %(v/v)isopropanol1reservoir
910 mMcAMP1reservoir
100.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 12, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→20 Å / Num. all: 38054 / Num. obs: 177444 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12
Reflection shellResolution: 1.82→20 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / % possible all: 98
Reflection
*PLUS
Num. obs: 38054 / % possible obs: 97.7 % / Redundancy: 4.7 % / Num. measured all: 177444

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GAP

3gap
PDB Unreleased entry


Resolution: 1.82→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3 1875 Random
Rwork0.227 --
obs0.228 38054 -
all-36380 -
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 66 216 3604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.265
X-RAY DIFFRACTIONs_from_restr_planes0.0253
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 1 / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.025

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