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- PDB-2bri: UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE ... -

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Basic information

Entry
Database: PDB / ID: 2bri
TitleUMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE ANALOG AMPPNP
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 / phosphorylation / 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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Uridylate kinase
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 5, 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4876
Polymers49,4262
Non-polymers1,0614
Water25214
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,46218
Polymers148,2796
Non-polymers3,18312
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)146.684, 146.684, 146.684
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: (0.31093, -0.81282, 0.4926), (-0.84032, -0.47725, -0.25708), (0.44405, -0.33401, -0.83142)
Vector: 125.57504, 241.52122, 77.0238)

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Components

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


Mass: 24713.166 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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.68 Å3/Da / Density % sol: 53.83 % / 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: 3→20 Å / Num. obs: 10646 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.19 Å / Redundancy: 7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.96 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 5157585.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUN LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.282 541 5.1 %RANDOM
Rwork0.217 ---
obs0.217 10646 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9638 Å2 / ksol: 0.338637 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 64 14 3530
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_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it5.232
X-RAY DIFFRACTIONc_scangle_it6.682.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 103 5.9 %
Rwork0.314 1654 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ANP2.PARAMANP2.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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