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Open data
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Basic information
Entry | Database: PDB / ID: 1iho | ||||||
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Title | CRYSTAL APO-STRUCTURE OF PANTOTHENATE SYNTHETASE FROM E. COLI | ||||||
![]() | PANTOATE--BETA-ALANINE LIGASE | ||||||
![]() | LIGASE / Rossmann fold / dimer / apo / HIGH / KSMKS / flexible domains / multidomain | ||||||
Function / homology | ![]() pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | von Delft, F. / Lewendon, A. / Dhanaraj, V. / Blundell, T.L. / Abell, C. / Smith, A. | ||||||
![]() | ![]() Title: The crystal structure of E. coli pantothenate synthetase confirms it as a member of the cytidylyltransferase superfamily. Authors: von Delft, F. / Lewendon, A. / Dhanaraj, V. / Blundell, T.L. / Abell, C. / Smith, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.5 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.9 KB | Display | ![]() |
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Full document | ![]() | 464.3 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is completely represented by the dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 31639.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31663, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | ChemComp-TRS / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000 (4-6%), Tris buffer pH 8 (50 mM), VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 77294 / Num. obs: 81357 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.1 / Redundancy: 7 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 15.9 | ||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / Num. unique all: 6542 / Rsym value: 0.6 / % possible all: 78.5 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 87 % / Redundancy: 3 % / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: From experimental phases Resolution: 1.7→50 Å / Num. parameters: 2035 / Num. restraintsaints: 1823 Isotropic thermal model: Individual isotropic displacements, Overall anisotropic correction Cross valid method: FREE R / σ(F): 0 / σ(I): -999 / Stereochemistry target values: ENGH & HUBER Details: Initial refinement: Refmac Complete missing segements: Buster/TNT Final refinement: Shelxl; Phases were derived from 3 SeMet MAD wavelengths combined with a native, and then refined it ...Details: Initial refinement: Refmac Complete missing segements: Buster/TNT Final refinement: Shelxl; Phases were derived from 3 SeMet MAD wavelengths combined with a native, and then refined it against the native, but including experimental phases.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 Bsol: 3.2719 Å2 / ksol: 0.9297 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 4420 / Occupancy sum non hydrogen: 4956 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.29 / Rfactor obs: 0.26 |