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- PDB-3gg4: The crystal structure of glycerol kinase from Yersinia pseudotube... -

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Basic information

Entry
Database: PDB / ID: 3gg4
TitleThe crystal structure of glycerol kinase from Yersinia pseudotuberculosis
Componentsglycerol kinase
KeywordsTRANSFERASE / glycerol kinase / Yersinia pseudotuberculosis / structure genomics / 11200d1 / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / kinase activity / carbohydrate metabolic process / phosphorylation
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2240 / FGGY carbohydrate kinase, pentulose kinase / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2240 / FGGY carbohydrate kinase, pentulose kinase / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative carbohydrate kinase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHENIX AUTOSOl / Resolution: 2 Å
AuthorsZhang, Z. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of glycerol kinase from Yersinia pseudotuberculosis
Authors: Zhang, Z. / Swaminathan, S. / Burley, S.K.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: glycerol kinase
B: glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8863
Polymers123,6772
Non-polymers2091
Water14,574809
1
A: glycerol kinase


Theoretical massNumber of molelcules
Total (without water)61,8381
Polymers61,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0482
Polymers61,8381
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: glycerol kinase
hetero molecules

A: glycerol kinase


Theoretical massNumber of molelcules
Total (without water)123,8863
Polymers123,6772
Non-polymers2091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area3640 Å2
ΔGint-18 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.789, 110.393, 80.952
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein glycerol kinase / Putative carbohydrate kinase


Mass: 61838.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: YPTB3592 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon+RIL-stratagene / References: UniProt: Q665C6
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→79.81 Å / Num. all: 97360 / Num. obs: 90545 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9553 / % possible all: 67.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXAUTOSOLmodel building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: PHENIX AUTOSOl / Resolution: 2→36.004 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 3507 5.01 %RANDOM
Rwork0.1982 ---
obs0.2006 69998 98.36 %-
all-97360 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.838 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 24.24 Å2
Baniso -1Baniso -2Baniso -3
1-11.93 Å2-2.6618 Å2-9.2681 Å2
2---0 Å20.6746 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→36.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8181 0 14 809 9004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02740.27731340.21332670X-RAY DIFFRACTION98
2.0274-2.05640.27041430.19272581X-RAY DIFFRACTION98
2.0564-2.08710.241350.18672698X-RAY DIFFRACTION98
2.0871-2.11970.24061630.18762592X-RAY DIFFRACTION98
2.1197-2.15440.26631240.20012661X-RAY DIFFRACTION98
2.1544-2.19160.30291450.19952618X-RAY DIFFRACTION98
2.1916-2.23140.29091320.19842654X-RAY DIFFRACTION98
2.2314-2.27430.25881500.19962656X-RAY DIFFRACTION98
2.2743-2.32070.29791350.20122659X-RAY DIFFRACTION98
2.3207-2.37120.27771370.20172650X-RAY DIFFRACTION98
2.3712-2.42630.26111400.20432667X-RAY DIFFRACTION99
2.4263-2.4870.26671230.20922676X-RAY DIFFRACTION99
2.487-2.55420.25251350.20232662X-RAY DIFFRACTION99
2.5542-2.62930.26171440.19582692X-RAY DIFFRACTION99
2.6293-2.71420.22121390.19772654X-RAY DIFFRACTION99
2.7142-2.81120.26591390.20622686X-RAY DIFFRACTION99
2.8112-2.92370.26551390.21052684X-RAY DIFFRACTION99
2.9237-3.05670.27051500.21682679X-RAY DIFFRACTION99
3.0567-3.21770.25931680.20362675X-RAY DIFFRACTION99
3.2177-3.41920.22581390.20012691X-RAY DIFFRACTION99
3.4192-3.68290.22641550.18362658X-RAY DIFFRACTION99
3.6829-4.05310.20311340.17922729X-RAY DIFFRACTION99
4.0531-4.63860.19471450.16832674X-RAY DIFFRACTION99
4.6386-5.84010.20761330.19092666X-RAY DIFFRACTION97
5.8401-36.01020.25221260.22272559X-RAY DIFFRACTION92

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