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- PDB-3hif: The crystal structure of apo wild type CAP at 3.6 A resolution. -

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Basic information

Entry
Database: PDB / ID: 3hif
TitleThe crystal structure of apo wild type CAP at 3.6 A resolution.
ComponentsCatabolite gene activator
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / cAMP binding domain / Activator / cAMP / cAMP-binding / DNA-binding / Nucleotide-binding / Transcription / Transcription regulation
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 / DNA binding / 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
DNA-binding transcriptional dual regulator CRP / cAMP-activated global transcriptional regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AVERAGING / Resolution: 3.59 Å
AuthorsSteitz, T.A. / Sharma, H. / Wang, J. / Kong, J. / Yu, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
Authors: Sharma, H. / Yu, S. / Kong, J. / Wang, J. / Steitz, T.A.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: 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
C: Catabolite gene activator
D: Catabolite gene activator
E: Catabolite gene activator
F: Catabolite gene activator


Theoretical massNumber of molelcules
Total (without water)142,0356
Polymers142,0356
Non-polymers00
Water00
1
A: Catabolite gene activator
B: Catabolite gene activator


Theoretical massNumber of molelcules
Total (without water)47,3452
Polymers47,3452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-40 kcal/mol
Surface area20900 Å2
MethodPISA
2
C: Catabolite gene activator
D: Catabolite gene activator


Theoretical massNumber of molelcules
Total (without water)47,3452
Polymers47,3452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-36 kcal/mol
Surface area21280 Å2
MethodPISA
3
E: Catabolite gene activator
F: Catabolite gene activator


Theoretical massNumber of molelcules
Total (without water)47,3452
Polymers47,3452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-37 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.291, 125.291, 224.677
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 23672.439 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: crp, S4387, SF3376 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P0ACK1, UniProt: P0ACJ8*PLUS

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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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: Protein was crystallized after it was concentrated to ~25 mg/ml and seeded with apo D138L mutant CAP., pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007 / Details: SI 111
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→48.06 Å / Num. all: 23643 / Num. obs: 22948 / % possible obs: 98.93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.456 / Rsym value: 0.525 / Net I/σ(I): 23.05
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.621

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Processing

Software
NameVersionClassification
HKL-2000data collection
DMmodel building
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: AVERAGING
Starting model: cAMP Binding Domain of CAP

Resolution: 3.59→48.06 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.881 / SU B: 132.978 / SU ML: 0.837 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.75 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31823 1217 5 %RANDOM
Rwork0.29492 ---
obs0.29608 22948 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.723 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å21.78 Å20 Å2
2--3.56 Å20 Å2
3----5.35 Å2
Refinement stepCycle: LAST / Resolution: 3.59→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 0 0 9456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0229600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.96812924
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.13951182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.34624.429420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.369151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4911560
X-RAY DIFFRACTIONr_chiral_restr0.0650.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216966
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_it0.1031.55904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.1929522
X-RAY DIFFRACTIONr_scbond_it0.16433696
X-RAY DIFFRACTIONr_scangle_it0.3014.53402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.594→3.687 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 91 -
Rwork0.418 1573 -
obs--93.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.05243.6225-1.67578.1234-0.27667.9562-0.0259-0.0766-0.08930.0332-0.19210.91380.606-0.88230.21791.68730.75060.16830.566-0.0451.4279-28.0732.83244.944
23.13213.0503-1.4239.87410.91355.1871-0.0460.4693-0.0816-0.02150.00540.61090.1889-0.50980.04061.37510.8571-0.02430.9061-0.04421.326-14.981-3.523.962
39.3531-0.2831-1.3249.01063.960611.2802-0.1948-1.1381-0.29160.8219-0.4166-0.7470.93750.33220.61151.8960.4185-0.10641.13950.18610.7658-24.863-25.28547.829
47.9239-3.4038-0.15964.16145.251512.255-0.4655-0.2482-0.290.32690.33180.59990.9908-0.64570.13371.9136-0.03290.17621.1603-0.02870.6663-42.321-25.7430.424
54.9041-1.6039-1.2499.56053.3616.33160.4320.58630.2093-0.869-0.63280.0405-0.1865-0.07950.20091.83621.20750.09810.81390.21991.2222.212-30.37517.934
68.342.6792-0.2735.72940.68487.146-0.43761.1043-0.5378-0.54330.29320.65640.4798-0.74240.14451.84310.93070.02990.7868-0.19361.3435-3.155-31.07121.845
714.94923.4506-6.5465.7434-6.20687.3239-0.54880.6520.93730.33390.6074-0.3095-0.06150.8633-0.05861.32490.43620.04111.0528-0.38391.018711.609-44.321-9.792
89.86752.7466-3.5134.2456-3.92035.50550.7395-0.6836-0.45040.6911-0.80570.2261.51420.34340.06612.08510.54890.13161.5787-0.2641.1231.849-58.1358.281
92.98370.9453-1.356710.303-3.97675.04680.0304-0.1607-0.34640.3521-0.110.6515-0.1563-0.66970.07961.57720.83350.22340.8541-0.12161.4837-39.58630.33843.385
103.83070.52191.39225.2178-0.34299.07520.0896-0.503-0.50290.8042-0.13950.2080.5198-0.4280.04992.04390.73390.12210.74640.14551.108-33.28947.91460.797
112.5248-3.5848-2.36168.04496.41165.3746-0.9196-0.1132-0.5325-0.6075-0.2523.6703-0.2247-2.6531.17172.82940.0685-0.10152.19970.12892.5634-46.12518.74573.115
122.4513-2.6255-2.15194.99792.75121.9803-0.3485-0.18290.22320.29240.6294-0.6825-0.82980.928-0.2812.9675-0.17520.17612.0040.10341.385-22.39924.26671.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 130
2X-RAY DIFFRACTION2B7 - 130
3X-RAY DIFFRACTION3A133 - 207
4X-RAY DIFFRACTION4B133 - 207
5X-RAY DIFFRACTION5C7 - 130
6X-RAY DIFFRACTION6D7 - 130
7X-RAY DIFFRACTION7C133 - 207
8X-RAY DIFFRACTION8D133 - 207
9X-RAY DIFFRACTION9E7 - 130
10X-RAY DIFFRACTION10F7 - 130
11X-RAY DIFFRACTION11E133 - 207
12X-RAY DIFFRACTION12F133 - 207

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