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- PDB-3ezw: Crystal Structure of a Hyperactive Escherichia coli Glycerol Kina... -

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Basic information

Entry
Database: PDB / ID: 3ezw
TitleCrystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices
ComponentsGlycerol kinase
KeywordsTRANSFERASE / GLYCEROL KINASE / GLYCEROL METABOLISM / ALLOSTERIC REGULATION / MICROFLUIDICS / IN SITU DATA COLLECTION / ATP-binding / Kinase / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / identical protein binding ...glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain ...FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAnderson, M.J. / DeLaBarre, B. / Dunten, P. / Brunger, A.T. / Quake, S.R.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.
Authors: Anderson, M.J. / DeLabarre, B. / Raghunathan, A. / Palsson, B.O. / Brunger, A.T. / Quake, S.R.
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionNov 4, 2008ID: 2P3R
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol kinase
B: Glycerol kinase
E: Glycerol kinase
G: Glycerol kinase
C: Glycerol kinase
D: Glycerol kinase
F: Glycerol kinase
H: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,86144
Polymers473,6378
Non-polymers2,22436
Water27,4911526
1
A: Glycerol kinase
B: Glycerol kinase
E: Glycerol kinase
G: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,91122
Polymers236,8184
Non-polymers1,09318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-47 kcal/mol
Surface area67900 Å2
MethodPISA
2
C: Glycerol kinase
D: Glycerol kinase
F: Glycerol kinase
H: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,94922
Polymers236,8184
Non-polymers1,13118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-40 kcal/mol
Surface area67590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.116, 114.260, 212.624
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABEGCDFH

#1: Protein
Glycerol kinase / / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 59204.598 Da / Num. of mol.: 8 / Mutation: G230D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3926, glpK, JW3897 / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P0A6F3, glycerol kinase

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Non-polymers , 5 types, 1562 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1526 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: microfluidic free interface diffusion / pH: 8.5
Details: 20% PEG 1500, 0.3 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL, pH 8.5, microfluidic free interface diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 250186 / % possible obs: 84 % / Redundancy: 5.9 % / Rsym value: 0.059 / Net I/σ(I): 36.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.225 / % possible all: 73.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GLF

1glf


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.652 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOLVENT GEOMETRY ABOUT THE MG WAS RESTRAINED USING MO6 IDEAL VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.22478 5032 2 %RANDOM
Rwork0.16673 ---
obs0.1679 246407 84.05 %-
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: 24.437 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20.59 Å2
2--0.97 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31113 0 133 1526 32772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02232003
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221653
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.94143350
X-RAY DIFFRACTIONr_angle_other_deg1.673352454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02453955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24723.8281531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.477155450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.76315258
X-RAY DIFFRACTIONr_chiral_restr0.1160.24769
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0235849
X-RAY DIFFRACTIONr_gen_planes_other0.0030.026665
X-RAY DIFFRACTIONr_mcbond_it1.1071.519572
X-RAY DIFFRACTIONr_mcbond_other0.3381.58111
X-RAY DIFFRACTIONr_mcangle_it1.872231503
X-RAY DIFFRACTIONr_scbond_it2.989312431
X-RAY DIFFRACTIONr_scangle_it4.6894.511847
LS refinement shellResolution: 2→2.034 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.277 227 -
Rwork0.18 10133 -
obs--72.27 %

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