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- PDB-1v8f: Crystal Structure of Pantoate-beta-Alanine (Pantothenate Syntheta... -

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Basic information

Entry
Database: PDB / ID: 1v8f
TitleCrystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8
ComponentsPantoate-beta-alanine ligase
KeywordsLIGASE / Rossmann Fold / Dimer / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBagautdinov, B. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8
Authors: Bagautdinov, B. / Tahirov, T.H.
History
DepositionJan 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)62,78517
Polymers61,4672
Non-polymers1,31815
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-55 kcal/mol
Surface area23570 Å2
MethodPISA
2
A: Pantoate-beta-alanine ligase
B: Pantoate-beta-alanine ligase
hetero molecules

A: Pantoate-beta-alanine ligase
B: Pantoate-beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,57034
Polymers122,9334
Non-polymers2,63730
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_763-x+2,-x+y+1,-z-4/31
Buried area14450 Å2
ΔGint-137 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.514, 88.514, 266.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe bilogical assembly is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pantoate-beta-alanine ligase / pantothenate synthetase


Mass: 30733.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: PanC / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: P83701, UniProt: Q5SHF5*PLUS, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 739 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8
Details: PEG4000, TRIS, lithium cloride, pH 8, MICROBATCH, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 15, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 48570 / Num. obs: 46607 / % possible obs: 95.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 7.33 / Num. unique all: 6079 / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1UFV

1ufv


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2357 -RANDOM
Rwork0.205 ---
all-46964 --
obs-44607 94.6 %-
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.04 Å24.24 Å20 Å2
2--8.04 Å20 Å2
3----16.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 80 724 5144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.9-1.990.2782610.2460.017547990.1
1.99-2.090.2592820.2150.015572493.9
2.09-2.220.2722770.2120.016584695.6
2.22-2.40.2463020.20.014591196.5
2.4-2.640.2572990.210.015600497.8
2.64-3.020.2483370.2010.014609998.4
3.02-3.80.2363000.1840.014606096.3
3.8-39.620.2742990.2140.016584187.8

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