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- PDB-3ll5: Crystal structure of T. acidophilum isopentenyl phosphate kinase ... -

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Basic information

Entry
Database: PDB / ID: 3ll5
TitleCrystal structure of T. acidophilum isopentenyl phosphate kinase product complex
ComponentsGamma-glutamyl kinase related protein
KeywordsTRANSFERASE / alternate mevalonate pathway / isopentenyl phsophate kinase / alpha-beta-alpha sandwich fold / product complex / Kinase
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Isopentenyl phosphate / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.987 Å
AuthorsMabanglo, M.F. / Hill, C.P.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: X-ray structures of isopentenyl phosphate kinase.
Authors: Mabanglo, M.F. / Schubert, H.L. / Chen, M. / Hill, C.P. / Poulter, C.D.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 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 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Gamma-glutamyl kinase related protein
B: Gamma-glutamyl kinase related protein
C: Gamma-glutamyl kinase related protein
D: Gamma-glutamyl kinase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,12312
Polymers112,4304
Non-polymers2,6938
Water4,324240
1
A: Gamma-glutamyl kinase related protein
C: Gamma-glutamyl kinase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5626
Polymers56,2152
Non-polymers1,3474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-25 kcal/mol
Surface area19900 Å2
MethodPISA
2
B: Gamma-glutamyl kinase related protein
D: Gamma-glutamyl kinase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5626
Polymers56,2152
Non-polymers1,3474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-29 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.104, 42.787, 134.895
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Gamma-glutamyl kinase related protein / Isopentenyl phosphate kinase


Mass: 28107.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: Ta0103 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: Q9HLX1

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Non-polymers , 5 types, 248 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-IP8 / Isopentenyl phosphate / 3-methylbut-3-en-1-yl dihydrogen phosphate


Mass: 166.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O4P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M PCB buffer (2:1:2 molar ratio of sodium propionate, sodium cacodylate, Bis-Tris propane, pH 6.0 containing 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 274K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97887 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 27, 2009
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 65826 / Redundancy: 1.8 % / Rsym value: 0.062 / Net I/σ(I): 9.48
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.062

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX1.6.1_357refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. acidophilum isopentenyl phosphate kinase solved by single wavelength anomalous diffraction

Resolution: 1.987→38.292 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 3342 5.08 %
Rwork0.193 --
obs0.1954 65826 95.96 %
all-69169 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.941 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5158 Å20 Å2-3.4756 Å2
2---1.3365 Å2-0 Å2
3---0.8207 Å2
Refinement stepCycle: LAST / Resolution: 1.987→38.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7261 0 164 240 7665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0217579
X-RAY DIFFRACTIONf_angle_d1.97510248
X-RAY DIFFRACTIONf_dihedral_angle_d17.7542872
X-RAY DIFFRACTIONf_chiral_restr0.1151134
X-RAY DIFFRACTIONf_plane_restr0.011285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9867-2.01510.28391150.22082150X-RAY DIFFRACTION80
2.0151-2.04510.26091630.19882613X-RAY DIFFRACTION97
2.0451-2.07710.25191410.18932573X-RAY DIFFRACTION96
2.0771-2.11110.24061360.19272606X-RAY DIFFRACTION97
2.1111-2.14750.27651170.19782609X-RAY DIFFRACTION96
2.1475-2.18660.28191170.19352582X-RAY DIFFRACTION96
2.1866-2.22860.26241270.1812608X-RAY DIFFRACTION96
2.2286-2.27410.22651360.18142564X-RAY DIFFRACTION95
2.2741-2.32360.26511200.18412539X-RAY DIFFRACTION95
2.3236-2.37760.21391430.18352574X-RAY DIFFRACTION95
2.3776-2.43710.28431330.1922508X-RAY DIFFRACTION94
2.4371-2.50290.27951230.19892578X-RAY DIFFRACTION94
2.5029-2.57660.28091300.2092509X-RAY DIFFRACTION93
2.5766-2.65970.28781450.21532541X-RAY DIFFRACTION94
2.6597-2.75480.26751480.20252560X-RAY DIFFRACTION95
2.7548-2.8650.2561540.19852581X-RAY DIFFRACTION96
2.865-2.99540.25041420.20512624X-RAY DIFFRACTION97
2.9954-3.15320.25011550.20282686X-RAY DIFFRACTION98
3.1532-3.35070.23591550.20082663X-RAY DIFFRACTION99
3.3507-3.60920.22281560.18382745X-RAY DIFFRACTION100
3.6092-3.97210.20821450.17872723X-RAY DIFFRACTION100
3.9721-4.5460.18791370.15252761X-RAY DIFFRACTION100
4.546-5.72450.181480.16692754X-RAY DIFFRACTION100
5.7245-38.29880.2241560.21882833X-RAY DIFFRACTION98

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