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- PDB-2jjx: THE CRYSTAL STRUCTURE OF UMP KINASE FROM BACILLUS ANTHRACIS (BA1797) -

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Basic information

Entry
Database: PDB / ID: 2jjx
TitleTHE CRYSTAL STRUCTURE OF UMP KINASE FROM BACILLUS ANTHRACIS (BA1797)
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PYRIMIDINE BIOSYNTHESIS / ATP-BINDING / URIDYLATE KINASE / NUCLEOTIDE-BINDING / OPPF / PYRH / KINASE / CYTOPLASM / OXFORD PROTEIN PRODUCTION FACILITY (OPPF) / STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
Function / homology
Function and homology information


UMP kinase / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / UMP kinase activity / 'de novo' CTP biosynthetic process / ATP binding / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / UMP kinase / Uridylate kinase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMeier, C. / Carter, L.G. / Mancini, E.J. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Crystal Structure of Ump Kinase from Bacillus Anthracis (Ba1797) Reveals an Allosteric Nucleotide-Binding Site.
Authors: Meier, C. / Carter, L.G. / Sainsbury, S. / Mancini, E.J. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M.
History
DepositionApr 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
Revision 1.4Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5347
Polymers84,9883
Non-polymers1,5464
Water2,558142
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,06814
Polymers169,9766
Non-polymers3,0928
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area19140 Å2
ΔGint-136.3 kcal/mol
Surface area69060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.300, 87.300, 383.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50059, 0.86567, 0.00523), (-0.86568, -0.50056, -0.00554), (-0.00218, -0.0073, 0.99997)82.788, 7.587, -0.43
2given(-0.49555, -0.86822, -0.02504), (0.86843, -0.49579, 0.00392), (-0.01582, -0.01981, 0.99968)49.819, -68.801, 0.222

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Components

#1: Protein URIDYLATE KINASE / UMP KINASE


Mass: 28329.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: Q81S73, UniProt: A0A6L7HKK4*PLUS, UMP kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 8
Details: 0.2 M LITHIUM SULPHATE, 10% POLYETHYLENE GLYCOL 3000, 0.1 M IMIDAZOLE (PH 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.886
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 21872 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 2.82→2.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8

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Processing

Software
NameClassification
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9D

1z9d


Resolution: 2.82→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: REGIONS 20-23 AND 171-176 IN EACH CHAIN ARE POORLY ORDERED AND CLASH BETWEEN SYMMETRY RELATED COPIES RESIDUE PHE106 IN A AND B CHAINS CLASH WITH EACH OTHER WHILE RESIDUE PHE106 IN C CHAIN ...Details: REGIONS 20-23 AND 171-176 IN EACH CHAIN ARE POORLY ORDERED AND CLASH BETWEEN SYMMETRY RELATED COPIES RESIDUE PHE106 IN A AND B CHAINS CLASH WITH EACH OTHER WHILE RESIDUE PHE106 IN C CHAIN HAS A SYMMETRY RELATED CLASH WITH ITSELF THE ACTIVE SITE OF EACH CHAIN CONTAINS UNMODELLED ELECTRON DENSITY PRESUMED TO BE ATP WEAKLY BOUND IN THE ABSENCE OF BOUND UMP.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1094 5 %RANDOM
Rwork0.2 ---
obs-21612 --
Refinement stepCycle: LAST / Resolution: 2.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 94 142 5909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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