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- PDB-3ek6: Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram... -

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Basic information

Entry
Database: PDB / ID: 3ek6
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 / ATP binding / cytosol
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
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.34 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 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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


Theoretical massNumber of molelcules
Total (without water)156,3426
Polymers156,3426
Non-polymers00
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uridylate kinase
C: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)52,1142
Polymers52,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-22 kcal/mol
Surface area20680 Å2
MethodPISA
3
B: Uridylate kinase
D: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)52,1142
Polymers52,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-25 kcal/mol
Surface area20950 Å2
MethodPISA
4
E: Uridylate kinase
F: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)52,1142
Polymers52,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.473, 120.098, 125.808
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
12B
22D
13E
23F
14A
24B
34C
15D
25E
35F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERAA3 - 2406 - 243
21GLUGLUSERSERCC3 - 2406 - 243
12METMETSERSERBB1 - 2404 - 243
22METMETSERSERDD1 - 2404 - 243
13GLUGLUARGARGEE3 - 2396 - 242
23GLUGLUARGARGFF3 - 2396 - 242
14GLUGLUSERSERAA3 - 2406 - 243
24GLUGLUSERSERBB3 - 2406 - 243
34GLUGLUSERSERCC3 - 2406 - 243
15GLUGLUARGARGDD3 - 2396 - 242
25GLUGLUARGARGEE3 - 2396 - 242
35GLUGLUARGARGFF3 - 2396 - 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na Citrate, 20% 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: BL13B1 / Wavelength: 0.963896, 0.979441
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9638961
20.9794411
ReflectionResolution: 2.33→86.71 Å / Num. obs: 71166 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Rsym value: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.27 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.34→29.35 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.237 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.24 / 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
Rfree0.24556 3603 5.1 %RANDOM
Rwork0.20709 ---
obs0.20899 67497 98.78 %-
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: 46.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10795 0 0 489 11284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210921
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.97914700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28651430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98123.304457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.447151963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.70615102
X-RAY DIFFRACTIONr_chiral_restr0.0860.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.35609
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.57503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.5864
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.524
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.08727217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.839311187
X-RAY DIFFRACTIONr_scbond_it1.08124013
X-RAY DIFFRACTIONr_scangle_it1.76333513
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
11A1790medium positional0.60.5
21B1804medium positional0.690.5
31E1783medium positional0.550.5
41A1790medium positional0.730.5
42B1790medium positional0.630.5
43C1790medium positional0.610.5
51D1783medium positional0.610.5
52E1783medium positional0.690.5
53F1783medium positional0.570.5
11A1790medium thermal0.662
21B1804medium thermal3.562
31E1783medium thermal0.382
41A1790medium thermal0.992
42B1790medium thermal1.442
43C1790medium thermal0.962
51D1783medium thermal2.292
52E1783medium thermal1.42
53F1783medium thermal0.972
LS refinement shellResolution: 2.338→2.399 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 241 -
Rwork0.26 4591 -
obs--91.95 %
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)
10.8166-0.58660.01141.03860.03440.64110.0133-0.07750.08050.05330.0346-0.13080.04790.0323-0.0479-0.101-0.0017-0.0105-0.0311-0.04120.003724.829445.878178.3957
20.37820.32010.12160.52710.08921.44830.035-0.0231-0.08710.0090.0214-0.02990.0654-0.1077-0.0564-0.0956-0.036-0.0096-0.02330.0086-0.0136-1.098929.033665.8927
30.4542-0.4156-0.03261.16510.62960.7131-0.0692-0.0768-0.0471-0.09260.03760.0446-0.1421-0.09630.0316-0.05680.0618-0.0166-0.0079-0.0274-0.0566-3.527171.498981.0913
40.71750.2952-0.16070.7793-0.70091.8925-0.16380.0759-0.1524-0.27250.1025-0.1091-0.15250.10710.06130.0517-0.14390.0796-0.0413-0.0651-0.061415.166743.601234.8562
51.29830.57750.05321.91481.63921.746-0.09260.14670.0771-0.5183-0.12380.2629-0.4124-0.3460.21640.16620.0721-0.15990.0097-0.0047-0.1025-11.620162.588837.7804
60.76430.83950.24271.7580.24081.3068-0.12970.00790.029-0.34250.2077-0.1557-0.340.0337-0.0780.168-0.04510.0821-0.1445-0.0322-0.0514.255283.363355.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 240
2X-RAY DIFFRACTION2B1 - 240
3X-RAY DIFFRACTION3C3 - 240
4X-RAY DIFFRACTION4D1 - 240
5X-RAY DIFFRACTION5E3 - 239
6X-RAY DIFFRACTION6F3 - 240

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