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- PDB-4rk6: Crystal structure of LacI family transcriptional regulator CCPA f... -

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Basic information

Entry
Database: PDB / ID: 4rk6
TitleCrystal structure of LacI family transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926, with bound glucose
ComponentsGlucose-resistance amylase regulator
KeywordsTRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / D-glucose
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Glucose-resistance amylase regulator
Similarity search - Component
Biological speciesWeissella paramesenteroides ATCC 33313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-resistance amylase regulator
B: Glucose-resistance amylase regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4454
Polymers65,0842
Non-polymers3602
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-1 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.564, 102.564, 128.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 300
2116B0 - 300

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999988, -8.0E-5, 0.004936), (0.00084, 0.982527, 0.186119), (-0.004865, 0.186121, -0.982515)83.83878, -2.81809, 27.00982

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Components

#1: Protein Glucose-resistance amylase regulator


Mass: 32542.125 Da / Num. of mol.: 2 / Fragment: UNP residues 53-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella paramesenteroides ATCC 33313 (bacteria)
Gene: ccpA, HMPREF0877_1426 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5RBT0
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.641 M malonic acid, 0.088 M ammonium citrate tribasic, 0.042 M succinic ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.641 M malonic acid, 0.088 M ammonium citrate tribasic, 0.042 M succinic acid, 0.105 M DL-malic acid, 0.14 M sodium acetate, 0.175 M sodium formate, 0.056 M ammonium tartrate dibasic, cryoprotectant = reservoir + 100 mM glucose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 67129 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 33.3
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.61 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.114 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19826 2066 3.1 %RANDOM
Rwork0.16757 ---
obs0.16854 64875 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 24 429 4681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194365
X-RAY DIFFRACTIONr_bond_other_d0.0010.024160
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9825944
X-RAY DIFFRACTIONr_angle_other_deg0.88639590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06225.795195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86115709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6331514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
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_it7.5625.0242168
X-RAY DIFFRACTIONr_mcbond_other7.4925.0182167
X-RAY DIFFRACTIONr_mcangle_it8.2427.8272707
X-RAY DIFFRACTIONr_mcangle_other8.2717.8342708
X-RAY DIFFRACTIONr_scbond_it15.8916.4392197
X-RAY DIFFRACTIONr_scbond_other15.8916.442197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.1129.4593230
X-RAY DIFFRACTIONr_long_range_B_refined16.16623.2855091
X-RAY DIFFRACTIONr_long_range_B_other16.33822.9854881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4090 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.442
LOOSE THERMAL4.7810
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 136 -
Rwork0.209 4835 -
obs--100 %

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