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- PDB-1zp6: Crystal Structure of Atu3015, a Putative Cytidylate Kinase from A... -

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Basic information

Entry
Database: PDB / ID: 1zp6
TitleCrystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62
Componentshypothetical protein Atu3015
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyAAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / Shikimate kinase / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsForouhar, F. / Abashidze, M. / Vorobiev, S.M. / Kuzin, A. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62
Authors: Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Kuzin, A. / Conover, K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 16, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Atu3015
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2142
Polymers21,1181
Non-polymers961
Water905
1
A: hypothetical protein Atu3015
hetero molecules

A: hypothetical protein Atu3015
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4274
Polymers42,2352
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Unit cell
Length a, b, c (Å)91.960, 91.960, 173.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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Components

#1: Protein hypothetical protein Atu3015


Mass: 21117.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8UBK1, UniProt: A9CEJ3*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.6 Å3/Da / Density % sol: 72.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 50 mM MES, 1140 mM ammonium sulfate, and 5 mM DTT., pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979756, 0.97930, 0.96817
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2005 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797561
20.97931
30.968171
ReflectionResolution: 3.2→30 Å / Num. all: 11738 / Num. obs: 11773 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.067 / Net I/σ(I): 24.24
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.25 / Rsym value: 0.357 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SDMSdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→29.08 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 229100 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1025 9.9 %RANDOM
Rwork0.253 ---
obs0.253 10367 88.4 %-
all-11738 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.5365 Å2 / ksol: 0.246345 e/Å3
Displacement parametersBiso mean: 70.6 Å2
Baniso -1Baniso -2Baniso -3
1-16.09 Å20 Å20 Å2
2--16.09 Å20 Å2
3----32.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 5 5 1365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 125 9.6 %
Rwork0.299 1176 -
obs--66.6 %

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