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- PDB-4a7x: Crystal structure of uridylate kinase from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4a7x
TitleCrystal structure of uridylate kinase from Helicobacter pylori
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE
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
URIDINE-5'-DIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChu, C.H. / Liu, M.H. / Chen, P.C. / Sun, Y.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of Helicobacter Pylori Uridylate Kinase: Insight Into Release of the Product Udp
Authors: Chu, C.H. / Chen, P.C. / Liu, M.H. / Li, Y.C. / Hsiao, C.D. / Sun, Y.J.
History
DepositionNov 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Dec 20, 2023Group: 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)158,86710
Polymers157,2516
Non-polymers1,6174
Water7,080393
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8213
Polymers52,4172
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-36.3 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: URIDYLATE KINASE
D: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2254
Polymers52,4172
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-35.8 kcal/mol
Surface area19610 Å2
MethodPISA
3
E: URIDYLATE KINASE
F: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8213
Polymers52,4172
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-34.1 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.136, 127.627, 93.181
Angle α, β, γ (deg.)90.00, 91.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26208.449 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SG13009 / References: UniProt: P56106, UMP kinase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 62731 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BND

2bnd


Resolution: 2.49→96.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 24.649 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27571 2994 5 %RANDOM
Rwork0.21311 ---
obs0.2163 56433 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å2-0.82 Å2
2---0.48 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.49→96.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10464 0 100 393 10957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.97614392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73251371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78625.138434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.409151976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8551554
X-RAY DIFFRACTIONr_chiral_restr0.0790.21721
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027675
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2321.56777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.236210883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74733898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0494.53509
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.945310675
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.492→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 180 -
Rwork0.286 3969 -
obs--93.22 %
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)
10.2537-0.08060.04820.0875-0.00140.10760.01650.0124-0.01190.0011-0.007-0.00280.0087-0.0003-0.00960.0317-0.002-0.03050.0256-0.00090.0127123.806-0.609964.686
20.25830.09330.02160.0580.00560.10620.0137-0.0092-0.00470.0069-0.0085-0.00080.0126-0.0077-0.00530.0353-0.0054-0.03080.0262-0.00060.011988.485-0.055370.8202
30.11520.00780.06680.10470.02180.220.0077-0.01170.00540.0141-0.0032-0.00010.0196-0.0142-0.00450.0359-0.0044-0.02790.0287-0.00160.009399.737118.09194.2106
40.1418-0.02050.10790.1196-0.02240.30230.00470.02390.0053-0.0097-0.0040.00150.01650.0141-0.00070.0293-0.0027-0.02740.03190.00010.0083112.573318.175441.4483
50.13540.11710.08510.33520.08510.1152-0.01180.00540.016-0.01320.00160.0202-0.01050.00480.01020.0302-0.0063-0.02990.0320.00250.011126.752642.439963.5677
60.1309-0.07960.07050.3756-0.070.1025-0.0029-0.00570.01810.0104-0.0113-0.0124-0.0024-0.00320.01420.02710-0.02870.0313-0.00410.012585.452442.111372.1173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 240
2X-RAY DIFFRACTION2C1 - 240
3X-RAY DIFFRACTION3F1 - 240
4X-RAY DIFFRACTION4A1 - 240
5X-RAY DIFFRACTION5B1 - 240
6X-RAY DIFFRACTION6E1 - 240

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