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- PDB-4cyd: GlxR bound to cAMP -

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Basic information

Entry
Database: PDB / ID: 4cyd
TitleGlxR bound to cAMP
Components
  • PROBABLE EXPRESSION TAG
  • PROBABLE TRANSCRIPTION REGULATOR
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


kinase activity / nucleotide binding / regulation of DNA-templated transcription / DNA binding
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-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.82 Å
AuthorsTownsend, P.D. / Bott, M. / Cann, M.J. / Pohl, E.
CitationJournal: Plos One / Year: 2014
Title: The Crystal Structures of Apo and Camp-Bound Glxr from Corynebacterium Glutamicum Reveal Structural and Dynamic Changes Upon Camp Binding in Crp/Fnr Family Transcription Factors.
Authors: Townsend, P.D. / Jungwirth, B. / Pojer, F. / Bussmann, M. / Money, V.A. / Cole, S.T. / Puhler, A. / Tauch, A. / Bott, M. / Cann, M.J. / Pohl, E.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: 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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE TRANSCRIPTION REGULATOR
B: PROBABLE TRANSCRIPTION REGULATOR
C: PROBABLE TRANSCRIPTION REGULATOR
D: PROBABLE TRANSCRIPTION REGULATOR
F: PROBABLE EXPRESSION TAG
H: PROBABLE EXPRESSION TAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,67912
Polymers104,1786
Non-polymers1,5016
Water7,368409
1
B: PROBABLE TRANSCRIPTION REGULATOR
D: PROBABLE TRANSCRIPTION REGULATOR
F: PROBABLE EXPRESSION TAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7485
Polymers52,0893
Non-polymers6582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-29.7 kcal/mol
Surface area20470 Å2
MethodPISA
2
A: PROBABLE TRANSCRIPTION REGULATOR
C: PROBABLE TRANSCRIPTION REGULATOR
H: PROBABLE EXPRESSION TAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9327
Polymers52,0893
Non-polymers8434
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-31.7 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 102.660, 82.220
Angle α, β, γ (deg.)90.00, 108.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROBABLE TRANSCRIPTION REGULATOR / GLXR


Mass: 24760.240 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: H7C677
#2: Protein/peptide PROBABLE EXPRESSION TAG


Mass: 2568.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#3: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.46 Å3/Da / Density % sol: 49.92 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.82→29.4 Å / Num. obs: 88615 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.3

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.82→29.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.271 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24553 4447 5 %RANDOM
Rwork0.18934 ---
obs0.19216 84141 98.35 %-
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: 37.898 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å21.07 Å2
2--0.43 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.82→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7122 0 100 409 7631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197460
X-RAY DIFFRACTIONr_bond_other_d0.0020.025045
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.97110145
X-RAY DIFFRACTIONr_angle_other_deg1.073312228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13922.791344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.642151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111584
X-RAY DIFFRACTIONr_chiral_restr0.1170.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021558
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: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 270 -
Rwork0.244 5829 -
obs--93.17 %

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