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- PDB-1z9d: Crystal structure of a putative uridylate kinase (UMP-kinase) fro... -

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Basic information

Entry
Database: PDB / ID: 1z9d
TitleCrystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes
Componentsuridylate kinase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T1668 / pyrH / putative uridylate kinase / UMP-kinase / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


UMP kinase / 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
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD aided by molecular replacement / Resolution: 2.8 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes
Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: 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 / refine / struct_biol
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)83,68812
Polymers82,8233
Non-polymers8659
Water1,58588
1
A: uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9925
Polymers27,6081
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8964
Polymers27,6081
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8003
Polymers27,6081
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
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)167,37624
Polymers165,6476
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18210 Å2
ΔGint-380 kcal/mol
Surface area53420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)161.288, 57.309, 94.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsUMP-Kinase from B. subtilis has a sequence identity of 40% to T1668 and is known to exist as a hexamer (a trimer of dimers). This fact has been experimentally tested via Gel filtration(C. Gagyi et. al. Eur. J. Biochem. 270, 3196-3204). However biologically active species are monomers. The hexamer can be generated by symmetry operation -X+1,-Y,Z.

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Components

#1: Protein uridylate kinase / E.C.2.7.4.- / UK / Uridine monophosphate kinase / UMP kinase


Mass: 27607.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pyrH / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3
References: UniProt: P65938, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 53.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M Ammonium sulfate, 0.15M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2004 / Details: Diamond monochromator and downstream mirror
RadiationMonochromator: Flat Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 38306 / Num. obs: 38306 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 11.04 % / Biso Wilson estimate: 59.5 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.05 / Num. unique all: 3849 / Rsym value: 0.382 / % possible all: 92.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD aided by molecular replacement
Resolution: 2.8→19.72 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 222033.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A molecular replacement solution was obtained using a model derived from pdb entry 1YBD. MR phases were used to locate Se sites. Experimental phases were calculated using a Se-substructure ...Details: A molecular replacement solution was obtained using a model derived from pdb entry 1YBD. MR phases were used to locate Se sites. Experimental phases were calculated using a Se-substructure containing 26 Se sites. Nine sulfate groups were located. Sulfates D4 - D9 mimic phosphate group of ATP at the ATP binding pocket.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1813 5.1 %RANDOM
Rwork0.215 ---
obs0.2151 35774 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.7658 Å2 / ksol: 0.318634 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.57 Å20 Å20 Å2
2--17.74 Å20 Å2
3----8.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 45 88 5485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 275 5.4 %
Rwork0.352 4841 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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