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- PDB-1iho: CRYSTAL APO-STRUCTURE OF PANTOTHENATE SYNTHETASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1iho
TitleCRYSTAL APO-STRUCTURE OF PANTOTHENATE SYNTHETASE FROM E. COLI
ComponentsPANTOATE--BETA-ALANINE LIGASE
KeywordsLIGASE / Rossmann fold / dimer / apo / HIGH / KSMKS / flexible domains / multidomain
Function / homology
Function and homology information


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
Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich ...Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pantothenate synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
Authorsvon Delft, F. / Lewendon, A. / Dhanaraj, V. / Blundell, T.L. / Abell, C. / Smith, A.
CitationJournal: Structure / Year: 2001
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
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANTOATE--BETA-ALANINE LIGASE
B: PANTOATE--BETA-ALANINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5265
Polymers63,2792
Non-polymers2463
Water11,061614
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.031, 78.075, 77.126
Angle α, β, γ (deg.)90.00, 103.71, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is completely represented by the dimer in the asymmetric unit.

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Components

#1: Protein PANTOATE--BETA-ALANINE LIGASE / PANTOTHENATE SYNTHETASE / PANTOATE ACTIVATING ENZYME


Mass: 31639.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panc / Plasmid: pUC19 PCL / Production host: Escherichia coli (E. coli) / Strain (production host): AT1371
References: UniProt: P31663, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1reservoir
24-6 %PEG40001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.970,0.8850,0.9791
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDateDetails
BRANDEIS - B41CCDMay 30, 1999Condensing Mirror Tunable Monochromator
BRANDEIS - B42CCDMay 30, 1999Condensing Mirror Tunable Monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2si(111)Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.8851
30.97911
41.11
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
SHELXL-97refinement
SHARPphasing
REFMACrefinement
ARPmodel building
BUSTERrefinement
TNTrefinement
SHELXmodel building
Omodel building
SnBphasing
MOSFLMdata reduction
CCP4(SCALA)data scaling
BUSTERphasing
TNTphasing
SHELXphasing
RefinementMethod to determine structure: MAD
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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 4062 5 %RANDOM 5%
Rwork0.2118 ---
all0.211 77295 --
obs0.211 81357 92.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Bsol: 3.2719 Å2 / ksol: 0.9297 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Refine analyzeOccupancy sum hydrogen: 4420 / Occupancy sum non hydrogen: 4956
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 20 614 4967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0227
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0
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

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