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- PDB-2a1f: Crystal Structure of Uridylate kinase -

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Basic information

Entry
Database: PDB / ID: 2a1f
TitleCrystal Structure of Uridylate kinase
ComponentsUridylate kinase
KeywordsTRANSFERASE / Uridylate kinase / PyrH / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Uridylate kinase
Authors: Gorman, J. / Shapiro, L.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)161,8286
Polymers161,8286
Non-polymers00
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Uridylate kinase
F: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)53,9432
Polymers53,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-24 kcal/mol
Surface area20460 Å2
MethodPISA
3
C: Uridylate kinase
D: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)53,9432
Polymers53,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-24 kcal/mol
Surface area21270 Å2
MethodPISA
4
A: Uridylate kinase
B: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)53,9432
Polymers53,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area19760 Å2
MethodPISA
5
B: Uridylate kinase
C: Uridylate kinase


Theoretical massNumber of molelcules
Total (without water)53,9432
Polymers53,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-13 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.369, 79.889, 79.899
Angle α, β, γ (deg.)94.85, 96.68, 96.88
Int Tables number1
Space group name H-MP1
DetailsHomoHexamer, generated by chains A, B, C, D, E, F

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Components

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


Mass: 26971.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: pyrH, smbA / Plasmid: modified pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P43890, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.99 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG4K, 0.1M Bis-Tris pH6.5, 0.6M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 105743 / Num. obs: 105743 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 2.88 / Num. unique all: 9707 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BNE

2bne


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.127 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.21 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26327 5258 5 %RANDOM
Rwork0.21031 ---
all0.213 105743 --
obs0.21296 105589 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.67 Å20.33 Å2
2---0.54 Å20.54 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10678 0 0 889 11567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210816
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210282
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.97514542
X-RAY DIFFRACTIONr_angle_other_deg0.801323840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13651394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44624.11438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.066152002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.911572
X-RAY DIFFRACTIONr_chiral_restr0.0720.21684
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022102
X-RAY DIFFRACTIONr_nbd_refined0.1940.22328
X-RAY DIFFRACTIONr_nbd_other0.180.210337
X-RAY DIFFRACTIONr_nbtor_refined0.1670.25190
X-RAY DIFFRACTIONr_nbtor_other0.0830.26306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2764
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.213
X-RAY DIFFRACTIONr_mcbond_it1.1271.58959
X-RAY DIFFRACTIONr_mcbond_other0.161.52938
X-RAY DIFFRACTIONr_mcangle_it1.268211020
X-RAY DIFFRACTIONr_scbond_it2.04234413
X-RAY DIFFRACTIONr_scangle_it2.9844.53522
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 349 -
Rwork0.253 6617 -
obs--87.13 %

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