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- PDB-2ij9: Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus -

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Basic information

Entry
Database: PDB / ID: 2ij9
TitleCrystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus
ComponentsUridylate kinase
KeywordsTRANSFERASE / KINASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics 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, 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
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPatskovsky, Y. / Chen, R. / Keefe, L.J. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus
Authors: Patskovsky, Y. / Chen, R. / Keefe, L.J. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridylate kinase
B: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9024
Polymers46,7102
Non-polymers1922
Water0
1
A: Uridylate kinase
B: Uridylate kinase
hetero molecules

A: Uridylate kinase
B: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8048
Polymers93,4204
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Unit cell
Length a, b, c (Å)94.277, 94.277, 186.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METTYRAA1 - 1421 - 142
21METTYRBB1 - 1421 - 142
32VALSERAA153 - 168153 - 168
42VALSERBB153 - 168153 - 168
53VALALAAA179 - 219179 - 219
63VALALABB179 - 219179 - 219

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Components

#1: Protein Uridylate kinase / UK / Uridine monophosphate kinase / UMP kinase / putative dehydratase protein


Mass: 23354.996 Da / Num. of mol.: 2 / Mutation: R51S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: pyrH, AF_2042 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O28237, 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.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100MM SODIUM CITRATE, PH 4.5, 3.5M AMMONIUM SULFATE, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 23, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 23600 / Num. obs: 23600 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.093 / Rsym value: 0.081 / Net I/σ(I): 6.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 0.5 / Num. unique all: 1438 / Rsym value: 0.78 / % possible all: 54.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BRX
Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.834 / SU B: 19.287 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.69 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33021 595 3.2 %RANDOM
Rwork0.2828 ---
obs0.28428 17774 95.09 %-
all-17774 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.9 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--2.73 Å20 Å2
3----5.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 10 0 3234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223268
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9834418
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8975426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07324.828116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46515594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1321516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022326
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.31760
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.52282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.372
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.5641.52176
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.3223434
X-RAY DIFFRACTIONr_scbond_it17.96331192
X-RAY DIFFRACTIONr_scangle_it24.8234.5984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1502 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal2.263
LS refinement shellResolution: 2.9→2.974 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 54 -
Rwork0.378 1127 -
obs-1181 86.46 %

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