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- PDB-3rdi: Domain-domain flexibility leads to allostery within the camp rece... -

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Basic information

Entry
Database: PDB / ID: 3rdi
TitleDomain-domain flexibility leads to allostery within the camp receptor protein (CRP)
ComponentsCatabolite gene activator
KeywordsTRANSCRIPTION REGULATOR / CAMP RECEPTOR PROTEIN (CRP) / ALLOSTERY / DNA BINDING CYCLIC AMP / CATABOLITE ACTIVATOR PROTEIN (CAP) / DNA BINDING PROTEIN
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: 2.95 Å
AuthorsKnapp, J. / White, M.A. / Lee, J.C.
Citation
Journal: To be Published
Title: Domain-Domain Flexibility Leads to Allostery within the Cam Receptor Protein (Crp)
Authors: Knapp, J. / White, M.A. / Lee, J.C.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of a Complex of Catabolite Gene Activator Protein and Cyclic AMP at 2.5 A Resolution
Authors: Weber, I.T. / Steitz, T.A.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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_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: Catabolite gene activator
B: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1234
Polymers47,4652
Non-polymers6582
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-39 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.160, 92.750, 104.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Catabolite gene activator / cAMP receptor protein / cAMP regulatory protein


Mass: 23732.537 Da / Num. of mol.: 2 / Mutation: S63F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3357, cap, crp, csm, JW5702 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ACJ8
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% ETHANOL, 100MM TRIS, 3MM CAMP, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 9, 2007 / Details: CONFOCAL
RadiationMonochromator: MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. all: 9807 / Num. obs: 9807 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 134.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 20.6
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.45 / % possible all: 96.4

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Processing

Software
NameClassification
MACSCIENCEdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IL5

1il5


Resolution: 2.95→34.65 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1670547.31 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: 2 NCS GROUPS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 465 5 %THICK SHELLS
Rwork0.197 ---
all0.219 9233 --
obs0.219 9233 92.8 %-
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--4.27 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.95→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 44 3 3217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : _ / Rms dev position: _ / Weight Biso : 2 / Weight position: 2000

Ens-IDDom-IDNCS model details
11PMB/CNS-FLOATING B-FACTOR
22
LS refinement shellResolution: 2.95→3 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 19 5.4 %
Rwork0.328 332 -
obs--72.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PMB.PARAMPROTEIN_PMB.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM

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