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- PDB-1uky: SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FR... -

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Basic information

Entry
Database: PDB / ID: 1uky
TitleSUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


: / UMP/CMP kinase / CDP biosynthetic process / : / UMP kinase activity / Interconversion of nucleotide di- and triphosphates / AMP kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / 'de novo' pyrimidine nucleobase biosynthetic process ...: / UMP/CMP kinase / CDP biosynthetic process / : / UMP kinase activity / Interconversion of nucleotide di- and triphosphates / AMP kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / 'de novo' pyrimidine nucleobase biosynthetic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
UMP-CMP kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.13 Å
AuthorsMueller-Dieckmann, H.-J. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase.
Authors: Muller-Dieckmann, H.J. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The Structure of Uridylate Kinase with its Substrates, Showing the Transition State Geometry
Authors: Mueller-Dieckmann, H.-J. / Schulz, G.E.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6883
Polymers22,8341
Non-polymers8542
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.200, 64.200, 185.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: CIS PROLINE - PRO 106

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Components

#1: Protein URIDYLATE KINASE


Mass: 22834.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P15700, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE COMPLEX CONTAINS AN ADP AT THE ATP-BINDING SITE AND A MIXTURE OF ADP AND AMP AT THE NMP-BINDING SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mluridylate kinase1drop
210 %(w/v)PEG33501drop
30.02 %n-octyl-beta-D-glucoside1drop
41.5-2.0 mMATP1dropor ADP
550 mMpotassium phosphate1drop
615 %(w/v)PEG33501reservoir
750 mMpotassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.13 Å / Num. obs: 12091 / % possible obs: 91 % / Num. measured all: 32483
Reflection shell
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 2.19 Å / % possible obs: 64 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.13→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.178 -
obs0.178 12091
Refinement stepCycle: LAST / Resolution: 2.13→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 54 101 1711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

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