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- PDB-2j4l: Crystal structure of uridylate kinase from Sulfolobus solfataricu... -

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Basic information

Entry
Database: PDB / ID: 2j4l
TitleCrystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / UMP KINASE / NUCLEOSIDE MONOPHOSPHATE KINASE / PYRIMIDINE NUCLEOTIDE SYNTHESIS / ASPARTOKINASE FOLD
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Uridylate kinase, archaeal/spirochete, putative / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJensen, K.S. / Johansson, E. / Jensen, K.F.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of GTP Stimulation
Authors: Jensen, K.S. / Johansson, E. / Jensen, K.F.
History
DepositionSep 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
D: URIDYLATE KINASE
E: URIDYLATE KINASE
F: URIDYLATE KINASE
G: URIDYLATE KINASE
H: URIDYLATE KINASE
I: URIDYLATE KINASE
J: URIDYLATE KINASE
K: URIDYLATE KINASE
L: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,18231
Polymers300,20212
Non-polymers5,98019
Water00
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
D: URIDYLATE KINASE
E: URIDYLATE KINASE
F: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,10316
Polymers150,1016
Non-polymers3,00210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: URIDYLATE KINASE
H: URIDYLATE KINASE
I: URIDYLATE KINASE
J: URIDYLATE KINASE
K: URIDYLATE KINASE
L: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,07915
Polymers150,1016
Non-polymers2,9789
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)224.750, 79.030, 223.470
Angle α, β, γ (deg.)90.00, 96.56, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99684, 0.01015, -0.07877), (-0.02143, -0.98939, 0.1437), (-0.07648, 0.14493, 0.98648)-101.20412, 11.6296, -4.60986
2given(-0.14887, -0.54525, 0.82495), (-0.71678, 0.63421, 0.28983), (-0.68122, -0.54816, -0.48524)14.53205, -10.57962, -154.22807
3given(0.05991, 0.71699, 0.69451), (0.6896, -0.53277, 0.49052), (0.72171, 0.44954, -0.52635)11.83592, 73.76672, -91.76787
4given(0.21366, 0.59138, -0.77757), (0.61948, -0.69747, -0.36024), (-0.75537, -0.40472, -0.51538)-102.58392, 0.57904, -160.74702
5given(-0.1171, -0.75505, -0.64513), (-0.56014, 0.58663, -0.58491), (0.82008, 0.29286, -0.49163)-105.56078, -75.6161, -84.30929
6given(-0.80433, -0.58727, 0.09038), (-0.58845, 0.7662, -0.2582), (0.08238, -0.26086, -0.96185)-23.71639, -25.85692, -111.89214
7given(0.78188, 0.62063, 0.05907), (0.62217, -0.78281, -0.01068), (0.03961, 0.04511, -0.9982)48.19455, 53.82608, -117.28518
8given(0.5118, 0.02416, -0.85877), (-0.33262, 0.92721, -0.17215), (0.7921, 0.37375, 0.48258)-40.44608, -6.42438, 41.02373
9given(-0.42444, -0.20793, -0.88126), (0.35076, -0.93504, 0.05168), (-0.83476, -0.28717, 0.4698)-86.07069, 46.16991, -37.13826
10given(-0.59448, -0.0787, 0.80025), (0.51198, -0.80445, 0.30123), (0.62005, 0.58879, 0.51852)44.25107, 74.61203, 35.58593
11given(0.5015, 0.24923, 0.82848), (-0.52076, 0.85166, 0.05903), (-0.69087, -0.46104, 0.55689)98.35564, 3.6361, -22.70943

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Components

#1: Protein
URIDYLATE KINASE / UK / URIDINE MONOPHOSPHATE KINASE / UMP KINASE


Mass: 25016.873 Da / Num. of mol.: 12 / Fragment: RESIDUES 2-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97ZE2, UMP kinase
#2: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
Sequence detailsTHE CRYSTALLIZED ENZYME WAS PREPARED WITH ONLY ONE MET RESIDUE IN THE N-TERMINAL, IN CONTRAST TO ...THE CRYSTALLIZED ENZYME WAS PREPARED WITH ONLY ONE MET RESIDUE IN THE N-TERMINAL, IN CONTRAST TO THE DATABASE SEQUENCE.

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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: 3.32 Å3/Da / Density % sol: 60.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK, 2 MM UTP, 5 MM MGCL2 MIXED WITH 2UL MOTHER SOLUTION. MOTHER SOLUTION: 1.8 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.8. ...Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK, 2 MM UTP, 5 MM MGCL2 MIXED WITH 2UL MOTHER SOLUTION. MOTHER SOLUTION: 1.8 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.8. HANGIGN DROP VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2005 / Details: MULTILAYER MIRRORS
RadiationMonochromator: BENT GERMANIUM CRYSTAL, HORIZONTALLY FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.8→40.52 Å / Num. obs: 92163 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / % possible all: 85.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS

Resolution: 2.8→29.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1895858.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4593 5 %RANDOM
Rwork0.246 ---
obs0.246 91357 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7833 Å2 / ksol: 0.307533 e/Å3
Displacement parametersBiso mean: 76.9 Å2
Baniso -1Baniso -2Baniso -3
1--11.74 Å20 Å20.6 Å2
2--28.4 Å20 Å2
3----16.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å65 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19258 0 355 0 19613
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
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_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 671 4.9 %
Rwork0.389 13164 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4UDPUTP_PAR.TXTUDPUTP_TOP.TXT
X-RAY DIFFRACTION5ION.PARAMION.TOP

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