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- PDB-4i02: structure of the mutant Catabolite gene activator protein V140A -

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Basic information

Entry
Database: PDB / ID: 4i02
Titlestructure of the mutant Catabolite gene activator protein V140A
ComponentsCatabolite gene activator
KeywordsTRANSCRIPTION / DNA binding
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
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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 ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPohl, E. / Townsend, P.D. / Rodgers, T. / Burnell, D. / McLeish, T.C.B. / Wilson, M.R. / Cann, M.J.
CitationJournal: Plos Biol. / Year: 2013
Title: Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.
Authors: Rodgers, T.L. / Townsend, P.D. / Burnell, D. / Jones, M.L. / Richards, S.A. / McLeish, T.C. / Pohl, E. / Wilson, M.R. / Cann, M.J.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
C: Catabolite gene activator
D: Catabolite gene activator
E: Catabolite gene activator
F: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,26215
Polymers150,3006
Non-polymers2,9639
Water16,700927
1
A: Catabolite gene activator
E: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0875
Polymers50,1002
Non-polymers9883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-37 kcal/mol
Surface area20140 Å2
MethodPISA
2
B: Catabolite gene activator
hetero molecules

C: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0875
Polymers50,1002
Non-polymers9883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3070 Å2
ΔGint-37 kcal/mol
Surface area20610 Å2
MethodPISA
3
D: Catabolite gene activator
hetero molecules

F: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0875
Polymers50,1002
Non-polymers9883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area3140 Å2
ΔGint-36 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.260, 50.190, 276.322
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLYAA3 - 20815 - 220
21LEULEUGLYGLYBB3 - 20815 - 220
12ASPASPGLYGLYAA9 - 20821 - 220
22ASPASPGLYGLYCC9 - 20821 - 220
13LEULEUGLYGLYAA3 - 20815 - 220
23LEULEUGLYGLYDD3 - 20815 - 220
14ASPASPGLYGLYAA9 - 20821 - 220
24ASPASPGLYGLYEE9 - 20821 - 220
15ASPASPGLYGLYAA9 - 20821 - 220
25ASPASPGLYGLYFF9 - 20821 - 220
16ASPASPGLYGLYBB9 - 20821 - 220
26ASPASPGLYGLYCC9 - 20821 - 220
17METMETTHRTHRBB1 - 20913 - 221
27METMETTHRTHRDD1 - 20913 - 221
18ASPASPGLYGLYBB9 - 20821 - 220
28ASPASPGLYGLYEE9 - 20821 - 220
19ASPASPGLYGLYBB9 - 20821 - 220
29ASPASPGLYGLYFF9 - 20821 - 220
110ASPASPGLYGLYCC9 - 20821 - 220
210ASPASPGLYGLYDD9 - 20821 - 220
111ASPASPTHRTHRCC9 - 20921 - 221
211ASPASPTHRTHREE9 - 20921 - 221
112ASPASPTHRTHRCC9 - 20921 - 221
212ASPASPTHRTHRFF9 - 20921 - 221
113ASPASPGLYGLYDD9 - 20821 - 220
213ASPASPGLYGLYEE9 - 20821 - 220
114ASPASPGLYGLYDD9 - 20821 - 220
214ASPASPGLYGLYFF9 - 20821 - 220
115ASPASPTHRTHREE9 - 20921 - 221
215ASPASPTHRTHRFF9 - 20921 - 221

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 25049.922 Da / Num. of mol.: 6 / Mutation: V140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: crp, cap, csm, b3357, 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.: 9 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7-10% PEG3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9687 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2012
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 1.75→137.74 Å / Num. all: 160888 / Num. obs: 152519 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.795 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→48.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.941 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21572 7906 4.9 %RANDOM
Rwork0.18483 ---
all0.18635 160888 --
obs0.18635 152519 99.52 %-
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: 24.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.11 Å2
2---0.03 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 198 927 10593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.99113383
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80551221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95224.404411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.502151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg201560
X-RAY DIFFRACTIONr_chiral_restr0.1180.21549
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217169
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2450.07
12B2450.07
21A2150.09
22C2150.09
31A2420.07
32D2420.07
41A2250.1
42E2250.1
51A2110.1
52F2110.1
61B2210.1
62C2210.1
71B2460.09
72D2460.09
81B2290.1
82E2290.1
91B2170.13
92F2170.13
101C2210.09
102D2210.09
111C2360.09
112E2360.09
121C2340.08
122F2340.08
131D2270.12
132E2270.12
141D2160.11
142F2160.11
151E2290.12
152F2290.12
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 571 -
Rwork0.263 10737 -
obs--97.38 %

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