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- PDB-2va1: Crystal structure of UMP kinase from Ureaplasma parvum -

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Basic information

Entry
Database: PDB / ID: 2va1
TitleCrystal structure of UMP kinase from Ureaplasma parvum
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / UMPK / KINASE / URIDYLATE KINASE / PYRIMIDINE BIOSYNTHESIS / AMINO ACID KINASE FAMILY
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, bacteria / 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
PHOSPHATE ION / Uridylate kinase
Similarity search - Component
Biological speciesUREAPLASMA PARVUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEgeblad-Welin, L. / Welin, M. / Wang, L. / Eriksson, S.
CitationJournal: FEBS J. / Year: 2007
Title: Structural and Functional Investigations of Ureaplasma Parvum Ump Kinase - a Potential Antibacterial Drug Target
Authors: Egeblad-Welin, L. / Welin, M. / Wang, L. / Eriksson, S.
History
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,10412
Polymers169,5346
Non-polymers5706
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18670 Å2
ΔGint-163 kcal/mol
Surface area64760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.753, 96.552, 96.270
Angle α, β, γ (deg.)90.00, 105.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLYAA5 - 16026 - 181
21ARGARGGLYGLYBB5 - 16026 - 181
31ARGARGGLYGLYCC5 - 16026 - 181
41ARGARGGLYGLYDD5 - 16026 - 181
51ARGARGGLYGLYEE5 - 16026 - 181
61ARGARGGLYGLYFF5 - 16026 - 181
12VALVALTYRTYRAA193 - 230214 - 251
22VALVALTYRTYRBB193 - 230214 - 251
32VALVALTYRTYRCC193 - 230214 - 251
42VALVALTYRTYRDD193 - 230214 - 251
52VALVALTYRTYREE193 - 230214 - 251
62VALVALTYRTYRFF193 - 230214 - 251

NCS oper:
IDCodeMatrixVector
1given(-0.5311, 0.655, -0.5375), (0.6344, -0.1131, -0.7647), (-0.5617, -0.7471, -0.3555)37.88, 51.32, 92.46
2given(0.5811, -0.4221, -0.6958), (-0.416, -0.8889, 0.1918), (-0.6995, 0.1779, -0.6922)47.42, -14.27, 116.3
3given(-0.1822, -0.4563, 0.871), (0.9568, -0.2865, 0.05003), (0.2267, 0.8424, 0.4888)-59.69, -4.664, 35.8
4given(-0.205, 0.9398, 0.2733), (-0.4304, -0.3374, 0.8372), (0.879, 0.05404, 0.4737)-17.5, -57.63, 35.54
5given(-0.6643, -0.7345, 0.139), (-0.7321, 0.6017, -0.3193), (0.1509, -0.3139, -0.9374)-9.552, 22.43, 132.6

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Components

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


Mass: 28255.668 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UREAPLASMA PARVUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PPX6, UMP kinase, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.4 Å3/Da / Density % sol: 47.9 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM FLUORIDE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→33.42 Å / Num. obs: 48558 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A1F

2a1f


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.868 / SU B: 11.9 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.122 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 167-175 DEPENDING ON SUBUNIT ARE DISORDERED, EXCEPT FOR SUBUNIT E.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2456 5.1 %RANDOM
Rwork0.232 ---
obs0.235 46149 99.9 %-
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: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.92 Å2
2--0.09 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10600 0 30 158 10788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.96314455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07751366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4926.562448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.484152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1571529
X-RAY DIFFRACTIONr_chiral_restr0.0730.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.24716
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.27478
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2324
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.51.57019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.754210999
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7534090
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2334.53456
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A776tight positional0.020.05
2B776tight positional0.020.05
3C776tight positional0.020.05
4D776tight positional0.020.05
5E776tight positional0.030.05
6F776tight positional0.020.05
1A703medium positional0.520.5
2B703medium positional0.510.5
3C703medium positional0.530.5
4D703medium positional0.490.5
5E703medium positional0.510.5
6F703medium positional0.560.5
1A776tight thermal0.040.5
2B776tight thermal0.040.5
3C776tight thermal0.040.5
4D776tight thermal0.040.5
5E776tight thermal0.040.5
6F776tight thermal0.040.5
1A703medium thermal0.272
2B703medium thermal0.282
3C703medium thermal0.272
4D703medium thermal0.262
5E703medium thermal0.272
6F703medium thermal0.32
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 176
Rwork0.275 3329

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