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- PDB-2a84: Crystal structure of A Pantothenate synthetase complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 2a84
TitleCrystal structure of A Pantothenate synthetase complexed with ATP
ComponentsPantoate--beta-alanine ligase
KeywordsLIGASE / protein-substrate 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)32,3327
Polymers31,5001
Non-polymers8326
Water5,278293
1
A: Pantoate--beta-alanine ligase
hetero molecules

A: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,66414
Polymers63,0002
Non-polymers1,66412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)118.953, 44.877, 82.125
Angle α, β, γ (deg.)90.00, 125.26, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 45287 / Num. obs: 45287 / % possible obs: 87.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.115 / Net I/σ(I): 30.7
Reflection shellResolution: 1.55→1.61 Å / % possible obs: 30.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 1580 / Num. unique all: 1580 / Χ2: 0.932 / % possible all: 30.8

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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: 1.55→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.687 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3683 8.1 %RANDOM
Rwork0.15 ---
all0.152 45261 --
obs0.152 45261 87.77 %-
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: 26.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.25 Å2
2---0.1 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 51 293 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222148
X-RAY DIFFRACTIONr_bond_other_d0.0010.022085
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9912933
X-RAY DIFFRACTIONr_angle_other_deg0.82734790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1975275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28422.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96815324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8971523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.2160.2456
X-RAY DIFFRACTIONr_nbd_other0.1890.22158
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21091
X-RAY DIFFRACTIONr_nbtor_other0.0830.21327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2210
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.219
X-RAY DIFFRACTIONr_mcbond_it2.65321757
X-RAY DIFFRACTIONr_mcbond_other0.6182561
X-RAY DIFFRACTIONr_mcangle_it2.98832217
X-RAY DIFFRACTIONr_scbond_it4.4914844
X-RAY DIFFRACTIONr_scangle_it6.3146716
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 100 -
Rwork0.419 951 -
all-1051 -
obs--27.95 %
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)
11.23050.126-0.350.35020.01881.01050.0016-0.09210.09270.0087-0.0167-0.0398-0.05550.10290.0151-0.17530.0015-0.0036-0.11270.0031-0.1225-10.5725.43430.725
20.88570.1045-0.49490.65280.11971.7812-0.05110.1281-0.0659-0.00330.01650.01490.1842-0.00970.0346-0.15660.01280.0099-0.0610.0072-0.1252-2.61-9.12111.042
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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