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- PDB-1gsi: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Basic information

Entry
Database: PDB / ID: 1gsi
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE
Function / homology
Function and homology information


TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å
AuthorsUrsby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Cryophotolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals
Authors: Ursby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: X-Ray Structure of Tmp Kinase from Mycobacterium Tuberculosis Complexed with Tmp at 1.95 A Resolution
Authors: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Analysis of the Thymidylate Kinase from Mycobacterium Tuberculosis
Authors: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
History
DepositionJan 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4749
Polymers22,6631
Non-polymers8128
Water4,756264
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94918
Polymers45,3252
Non-polymers1,62416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)76.225, 76.225, 134.264
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THYMIDYLATE KINASE / TMK


Mass: 22662.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: STARTING MODEL PDB ENTRY 1G3U
Crystal growpH: 6
Details: PROTEIN CRYSTALLIZED IN 1.4M AMMONIUM SULFATE, 100MM MES PH6, 2% PEG 2000, 25MM MAGNESIUM ACETATE 2MM BETA-MERCAPTOETHANOL, pH 6.00
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Li de La Sierra, I., (2000) Acta Crystallogr.,Sect., D56, 226.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.270-0.392 mMprotein1drop
22 mMdTMP1drop
31 mMdithiothreitol1drop
42 mMEDTA1drop
515 mMTris-HCl1droppH7.4
635 %ammonium sulfate1reservoir
72 %PEG20001reservoir
80.1 MMES1reservoirpH6.0
92 mMbeta-mercaptoethanol1reservoir
1025 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.75
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.6→25.2 Å / Num. obs: 30736 / % possible obs: 99.1 % / Redundancy: 8.2 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.076 / Net I/σ(I): 20.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.282 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 252502 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 98.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.282

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.6→25.19 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1568 5.1 %RANDOM
Rwork0.193 ---
obs0.193 30664 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3241 Å2 / ksol: 0.362529 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.32 Å20 Å2
2--0.67 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 49 264 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.873.5
X-RAY DIFFRACTIONc_mcangle_it2.514
X-RAY DIFFRACTIONc_scbond_it2.724
X-RAY DIFFRACTIONc_scangle_it3.564.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 280 5.6 %
Rwork0.231 4697 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACT.PARAMACT.TOP
X-RAY DIFFRACTION4TMP.PARTMP.TOP
Refinement
*PLUS
Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor obs: 0.231

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