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- PDB-1ufv: Crystal Structure Of Pantothenate Synthetase From Thermus Thermop... -

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Basic information

Entry
Database: PDB / ID: 1ufv
TitleCrystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8
ComponentsPantoate-beta-alanine ligase
KeywordsLIGASE / Structural Genomics / Dimer / Domains / Rossmann Fold / 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
Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / 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. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
History
DepositionJun 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,44610
Polymers61,8792
Non-polymers5678
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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)124,89320
Polymers123,7594
Non-polymers1,13416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_763-x+2,-x+y+1,-z-4/31
Buried area11180 Å2
ΔGint-106 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.558, 88.558, 266.974
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1551-

HOH

DetailsThe bilogical assembly is a dimer

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Components

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


Mass: 30939.727 Da / Num. of mol.: 2 / Mutation: V48A
Source method: isolated from a genetically manipulated source
Details: Mutation of VAL 48 to ALA / Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: PanC / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P83701, UniProt: Q5SHF5*PLUS, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 44.27 %
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: Feb 2, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 602701 / Num. obs: 602601 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 7.5 / Num. unique all: 3898 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N2E

1n2e


Resolution: 2.05→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement performed using anomalous f', f'' library file for Se, Cl at 1 Angstrom
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3480 -RANDOM
Rwork0.201 ---
all-73486 --
obs-70612 96.1 %-
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.18 Å25.74 Å20 Å2
2--8.18 Å20 Å2
3----16.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 33 478 4847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.05-2.140.343750.2950.018825389.6
2.14-2.260.3354380.2610.016849492.4
2.26-2.40.2923830.2380.015871894.4
2.4-2.580.2935050.2280.013886796.6
2.58-2.840.284280.2230.014896997.6
2.84-3.250.2754480.210.013905298.6

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