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- PDB-2a7x: Crystal Structure of A Pantothenate synthetase complexed with AMP -

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Basic information

Entry
Database: PDB / ID: 2a7x
TitleCrystal Structure of A Pantothenate synthetase complexed with AMP
ComponentsPantoate-beta-alanine ligase
KeywordsLIGASE / protein-product inhibitor complex / 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 / cytosol / cytoplasm
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
ADENOSINE MONOPHOSPHATE / 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 6, 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 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 1.4Aug 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)32,1285
Polymers31,5001
Non-polymers6274
Water5,639313
1
A: Pantoate-beta-alanine ligase
hetero molecules

A: Pantoate-beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,25510
Polymers63,0002
Non-polymers1,2558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)120.262, 44.944, 82.236
Angle α, β, γ (deg.)90.00, 125.56, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 313 / 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, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 / Date: Jan 1, 2004 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 34940 / Num. obs: 34940 / % possible obs: 88 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 33.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1835 / Rsym value: 0.22 / % possible all: 47

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MOP

1mop


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.643 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17456 2802 8 %RANDOM
Rwork0.14831 ---
all0.15043 32094 --
obs0.15043 32094 88.13 %-
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: 31.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.07 Å2
2--0.37 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 40 313 2387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9852913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27722.55886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.761523
X-RAY DIFFRACTIONr_chiral_restr0.1380.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2976
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5221411
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.37232209
X-RAY DIFFRACTIONr_scbond_it4.9574794
X-RAY DIFFRACTIONr_scangle_it7.1436704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 103 -
Rwork0.209 1198 -
obs-1301 44.85 %
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)
11.14760.2306-0.28930.68940.1390.87990.0203-0.07930.05540.0199-0.0293-0.0959-0.04470.07360.009-0.10890.0045-0.0075-0.13690.0139-0.0989-10.6735.20530.783
21.30220.317-0.63520.99860.28522.0433-0.03010.0744-0.07160.0278-0.0001-0.00390.1856-0.01340.0302-0.08760.01550.0096-0.09140.0126-0.114-2.412-9.15811.005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1863 - 186
2X-RAY DIFFRACTION2AA187 - 288187 - 288

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