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- PDB-3ek5: Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram... -

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Basic information

Entry
Database: PDB / ID: 3ek5
TitleUnique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium
ComponentsUridylate kinase
KeywordsTRANSFERASE / Xanthomonas campestris / UMPK crystal structure / unique GTP binding site / allosteric regulation / ATP-binding / Kinase / Nucleotide-binding / Pyrimidine biosynthesis
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytosol
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / 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
GUANOSINE-5'-TRIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsTu, J.-L. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium
Authors: Tu, J.-L. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)159,48212
Polymers156,3426
Non-polymers3,1396
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20350 Å2
ΔGint-90 kcal/mol
Surface area52600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.634, 119.638, 125.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
12B
22E
32F
13A
23B
14C
24D
15E
25F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA2 - 2395 - 242
21ARGARGCC2 - 2395 - 242
31ARGARGDD2 - 2395 - 242
12ARGARGBB2 - 2395 - 242
22ARGARGEE2 - 2395 - 242
32ARGARGFF2 - 2395 - 242
13ARGARGAA2 - 2395 - 242
23ARGARGBB2 - 2395 - 242
14SERSERCC2 - 2405 - 243
24SERSERDD2 - 2405 - 243
15ARGARGEE2 - 2395 - 242
25ARGARGFF2 - 2395 - 242

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Uridylate kinase / UK / Uridine monophosphate kinase / UMP kinase / UMPK


Mass: 26057.082 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: XC17 / Gene: pyrH, XCC1371 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59009, UMP kinase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na Citrate, 19.5% PEG 3350, 0.05M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 2.56→86.39 Å / Num. all: 55638 / Num. obs: 55392 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.05 / Net I/σ(I): 23.7
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5439 / Rsym value: 0.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EK6

3ek6


Resolution: 2.56→27.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.137 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.709 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that are not the terminal residues of the sequence. In all these instances the OXT was changed to N of the next residue
RfactorNum. reflection% reflectionSelection details
Rfree0.25157 2814 5.1 %RANDOM
Rwork0.20626 ---
obs0.20858 52509 98.95 %-
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: 55.136 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.56→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10785 0 192 507 11484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3822.00115012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84351429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42123.304457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.823151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39115102
X-RAY DIFFRACTIONr_chiral_restr0.0830.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.35582
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.57651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5802
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.348
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04127197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.755311179
X-RAY DIFFRACTIONr_scbond_it1.02524324
X-RAY DIFFRACTIONr_scangle_it1.76633833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1789medium positional0.620.5
12C1789medium positional0.680.5
13D1789medium positional0.620.5
21B1789medium positional0.740.5
22E1789medium positional0.680.5
23F1789medium positional0.690.5
31A1789medium positional0.640.5
41C1796medium positional0.580.5
51E1789medium positional0.580.5
11A1789medium thermal0.992
12C1789medium thermal1.162
13D1789medium thermal1.122
21B1789medium thermal2.592
22E1789medium thermal1.032
23F1789medium thermal1.732
31A1789medium thermal2.92
41C1796medium thermal1.042
51E1789medium thermal0.592
LS refinement shellResolution: 2.56→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 184 -
Rwork0.324 3531 -
obs--91.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5456-0.2217-0.1050.897-0.08250.69970.0353-0.0073-0.01410.0651-0.01970.0733-0.0450.005-0.0156-0.1155-0.01120.0055-0.05080.0218-0.0067-24.470513.747214.8793
20.3475-0.56530.17551.2977-0.41280.8379-0.0674-0.07670.0669-0.09560.0302-0.03020.18190.12510.0373-0.09760.05890.0315-0.00510.0403-0.03963.4012-12.410617.7926
30.31250.3667-0.07240.4597-0.31491.81360.0348-0.0380.04910.007-0.03450.0697-0.14230.1539-0.0003-0.1212-0.0656-0.0093-0.03520.00020.00421.483430.35772.7161
40.42050.27560.13360.61750.31441.3616-0.15220.11680.1045-0.20580.09630.02710.0961-0.1250.05590.0601-0.1596-0.064-0.04350.0401-0.0737-14.02215.7806-29.0058
50.68160.3914-0.21020.6857-0.20811.7039-0.0471-0.08650.0433-0.24710.12210.02670.5061-0.042-0.0750.1606-0.0458-0.0347-0.14540.0145-0.0798-14.3074-23.9887-7.5938
61.14270.473-0.00770.7808-0.77391.1071-0.13680.1642-0.0257-0.3378-0.0092-0.10190.39750.31550.14610.14750.04910.1493-0.00140.024-0.075312.3284-3.4219-25.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 239
2X-RAY DIFFRACTION2B2 - 240
3X-RAY DIFFRACTION3C2 - 240
4X-RAY DIFFRACTION4D2 - 240
5X-RAY DIFFRACTION5E2 - 240
6X-RAY DIFFRACTION6F2 - 239

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