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- PDB-2a88: Crystal structure of A Pantothenate synthetase, apo enzyme in C2 ... -

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Basic information

Entry
Database: PDB / ID: 2a88
TitleCrystal structure of A Pantothenate synthetase, apo enzyme in C2 space group
ComponentsPantoate--beta-alanine ligase
KeywordsLIGASE / dimer / Rossmann fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / 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 / 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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Biochemistry / Year: 2006
Title: Crystal Structure of the Pantothenate Synthetase from Mycobacterium tuberculosis, Snapshots of the Enzyme in Action.
Authors: Wang, S. / Eisenberg, D.
#1: Journal: Protein Sci. / Year: 2003
Title: Crystal structures of a pantothenate synthetase and its complexes with substrates and a reaction intermediate
Authors: Wang, S. / Eisenberg, D.
History
DepositionJul 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7804
Polymers31,5001
Non-polymers2803
Water5,170287
1
A: Pantoate--beta-alanine ligase
hetero molecules

A: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5618
Polymers63,0002
Non-polymers5616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)119.818, 44.983, 82.136
Angle α, β, γ (deg.)90.00, 125.50, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological assembly is a dimer by the operation: -x, y, 1-z

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Components

#1: Protein Pantoate--beta-alanine ligase / Pantothenate synthetase / Pantoate activating enzyme


Mass: 31500.100 Da / Num. of mol.: 1 / Mutation: T2A, E77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: panC / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3000, glycerol, isopropanol, magnesium chloride, lithium sulfate, imidazole, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 38461 / Num. obs: 38461 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.065 / Net I/σ(I): 21.3
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 88.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 3453 / Num. unique all: 3453 / Χ2: 0.925 / % possible all: 88.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MOP

1mop


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.959 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3108 8.1 %RANDOM
Rwork0.152 ---
all0.155 38442 --
obs0.155 38442 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.17 Å2
2--0.32 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 17 287 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222108
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.972875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22422.79186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93715324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8011522
X-RAY DIFFRACTIONr_chiral_restr0.1330.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021588
X-RAY DIFFRACTIONr_nbd_refined0.2150.2970
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.222
X-RAY DIFFRACTIONr_mcbond_it2.6121411
X-RAY DIFFRACTIONr_mcangle_it3.53432211
X-RAY DIFFRACTIONr_scbond_it5.5134757
X-RAY DIFFRACTIONr_scangle_it7.8756664
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 189 -
Rwork0.276 2312 -
all-2501 -
obs-2501 86.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45150.2731-0.49460.59720.18941.1860.0188-0.09990.0702-0.0065-0.0096-0.0943-0.06760.1319-0.0092-0.17040.00180.0004-0.21180.0088-0.1755-10.6315.1630.811
21.40410.3705-0.83630.83320.22392.4697-0.06490.0274-0.09850.0326-0.0063-0.00580.21050.00170.0712-0.15090.02170.0183-0.15250.0134-0.191-2.505-9.12611.031
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
113 - 1863 - 186
22187 - 289187 - 289

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