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- PDB-2zs9: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -

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Basic information

Entry
Database: PDB / ID: 2zs9
TitlePantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with ADP and Pantothenate
ComponentsPantothenate kinase
KeywordsTRANSFERASE / homodimer / COA biosynthesis / nucleotide binding / ATP-binding / Coenzyme A biosynthesis / Kinase
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PANTOTHENOIC ACID / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action
Authors: Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M.
History
DepositionSep 4, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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_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: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,15714
Polymers35,7051
Non-polymers1,45213
Water3,315184
1
A: Pantothenate kinase
hetero molecules

A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,31428
Polymers71,4102
Non-polymers2,90426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9780 Å2
ΔGint-113 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.194, 104.194, 90.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantothenate kinase / MtPanK / Pantothenic acid kinase


Mass: 35704.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: coaA (Rv1092c) / Plasmid: PET-28a(+) (NOVAGEN) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PAU / PANTOTHENOIC ACID / N-[(2R)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANOYL]-BETA-ALANINE


Type: peptide-like / Mass: 219.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M to 1.8M tri sodium citrate, 0.05M-0.1M sodium acetate, 7.5%-10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 16, 2006 / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 15934 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1554 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEV

2gev


Resolution: 2.7→34.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1480370.64 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 771 4.8 %RANDOM
Rwork0.203 ---
obs0.203 15912 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.4604 Å2 / ksol: 0.405514 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å28.25 Å20 Å2
2--5.92 Å20 Å2
3----10.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 93 184 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d2.2
X-RAY DIFFRACTIONc_mcbond_it4.251.5
X-RAY DIFFRACTIONc_mcangle_it6.592
X-RAY DIFFRACTIONc_scbond_it7.692
X-RAY DIFFRACTIONc_scangle_it11.012.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 100 3.9 %
Rwork0.282 2486 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramADP_GOL_PAU_PO3_DRGCNS.TOP
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ADP_GOL_PAU_PO3_DRGCNS.paramion.top

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