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- PDB-1rz3: Structure of a Possible Uridine Kinase from Bacillus stearothermo... -

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Basic information

Entry
Database: PDB / ID: 1rz3
TitleStructure of a Possible Uridine Kinase from Bacillus stearothermophilus
Componentshypothetical protein RBSTP0775
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Bacillus stearothermophilus / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


kinase activity / ATP binding / metal ion binding
Similarity search - Function
Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Rbstp0775 protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Joachimiak, A. / Wu, R.-Y. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of hypothetical protein RBSTP0775 from Bacillus stearothermophilus
Authors: Cuff, M.E. / Joachimiak, A. / Wu, R.-Y.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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 / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING. THIS ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING. THIS PROTEIN IS WIT DATABASE ID RBSTP0775.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein RBSTP0775
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5883
Polymers24,4891
Non-polymers992
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.010, 45.185, 107.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein RBSTP0775


Mass: 24489.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP0775 / Production host: Escherichia coli (E. coli) / References: UniProt: P84134
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-propanol, MES pH6.0, calcium acetate, ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97896, 0.97910
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 16, 2003
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.97911
ReflectionResolution: 1.9→34.45 Å / Num. all: 17505 / Num. obs: 17505 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2 / Limit h max: 23 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 56 / Limit l min: 0 / Observed criterion F max: 1218158.9 / Observed criterion F min: 8.7
Reflection shellResolution: 1.9→1.99 Å / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→34.45 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 886 5.1 %random
Rwork0.203 ---
all0.203 17870 --
obs0.203 17505 98 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 67.5071 Å2 / ksol: 0.372362 e/Å3
Displacement parametersBiso max: 82.6 Å2 / Biso mean: 28.35 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--3.44 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 5 217 1786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.67
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.292864.20.23219790.0322205206593.7
1.99-2.090.2471215.60.19120380.0222177215999.2
2.09-2.220.21044.70.19320880.022200219299.6
2.22-2.390.2641155.30.20220740.0252210218999
2.39-2.630.2191054.70.20821060.0212229221199.2
2.63-3.020.2481115.10.20420800.0242231219198.2
3.02-3.80.2431245.60.19120900.0222260221498
3.8-34.450.231205.30.20921640.0212376228496.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ligand.paramligand.top

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