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- PDB-2brx: UMP KINASE FROM PYROCOCCUS FURIOSUS WITHOUT LIGANDS -

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Basic information

Entry
Database: PDB / ID: 2brx
TitleUMP KINASE FROM PYROCOCCUS FURIOSUS WITHOUT LIGANDS
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / UMP KINASE / AMINO ACID KINASE / PHOSPHORYL GROUP TRANSFER / PYRIMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Uridylate kinase, archaeal/spirochete, putative / 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 speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMarco-Marin, C. / Gil-Ortiz, F. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Pyrococcus Furiosus Ump Kinase Provides Insight Into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis.
Authors: Marco-Marin, C. / Gil-Ortiz, F. / Rubio, V.
History
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URIDYLATE KINASE
B: URIDYLATE KINASE


Theoretical massNumber of molelcules
Total (without water)53,1322
Polymers53,1322
Non-polymers00
Water1,856103
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE

A: URIDYLATE KINASE
B: URIDYLATE KINASE

A: URIDYLATE KINASE
B: URIDYLATE KINASE


Theoretical massNumber of molelcules
Total (without water)159,3956
Polymers159,3956
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
MethodPQS
Unit cell
Length a, b, c (Å)144.949, 144.949, 144.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.30291, -0.83757, 0.45466), (-0.84151, -0.459, -0.28491), (0.44732, -0.2963, -0.84387)
Vector: 128.52126, 237.92346, 71.70589)

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Components

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


Mass: 26565.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PUKPFU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8U122, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.59 Å3/Da / Density % sol: 52.15 % / Description: NOT DEPOSITED YET
Crystal growpH: 8 / Details: 3.5 M SODIUM FORMATE, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979471
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2003 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979471 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19894 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.73 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4462683.66 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1011 5.1 %RANDOM
Rwork0.203 ---
obs0.203 19894 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6518 Å2 / ksol: 0.356623 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 0 103 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 138 4.2 %
Rwork0.236 3123 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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