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- PDB-4del: Active site loop dynamics of a class IIa fructose 1,6-bisphosphat... -

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Basic information

Entry
Database: PDB / ID: 4del
TitleActive site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / CLASS II FRUCTOSE-1 / 6-BISPHOSPHATE ALDOLASE / ZINC ENZYME / DIHYDROXYACETONE / GLYCERALDEHYDE-3-PHOSPHATE / ALDOL CONDENSATION / GLYCOLYSIS / METAL-BINDING / phosphoglycolohydroxamate
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / zymogen binding / cell wall / peptidoglycan-based cell wall / glycolytic process / zinc ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOGLYCOLOHYDROXAMIC ACID / Fructose-bisphosphate aldolase / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPegan, S.D. / Mesecar, A.D.
CitationJournal: Biochemistry / Year: 2013
Title: Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.
Authors: Pegan, S.D. / Rukseree, K. / Capodagli, G.C. / Baker, E.A. / Krasnykh, O. / Franzblau, S.G. / Mesecar, A.D.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_special_symmetry / 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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details / _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: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9427
Polymers37,2761
Non-polymers6666
Water9,242513
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,76928
Polymers149,1044
Non-polymers2,66524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area19860 Å2
ΔGint-403 kcal/mol
Surface area46430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.797, 119.605, 164.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-943-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fructose-bisphosphate aldolase / / FBP aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase


Mass: 37276.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: fba, MT0379, MTCY13E10.25c, Rv0363c / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P67475, UniProt: P9WQA3*PLUS, fructose-bisphosphate aldolase

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Non-polymers , 6 types, 519 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 4.07 Å3/Da / Density % sol: 69.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 26% PEG 300, 0.1 M sodium acetate, 2mM phosphoglycolohydroxamate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2009
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→93.9 Å / Num. all: 79039 / Num. obs: 78320 / % possible obs: 94 %
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.2 / % possible all: 77.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EKL

3ekl


Resolution: 1.58→49.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2054 / WRfactor Rwork: 0.1885 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8645 / SU R Cruickshank DPI: 0.0717 / SU Rfree: 0.0708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 3910 5 %RANDOM
Rwork0.1885 ---
obs0.1893 78207 93.9 %-
all-79039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 24.0601 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---1.55 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 36 513 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222838
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9623869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.0295382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99425.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34215460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.847158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022188
X-RAY DIFFRACTIONr_nbd_refined0.2110.21478
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2377
X-RAY DIFFRACTIONr_metal_ion_refined0.4730.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_mcbond_it0.5641.51808
X-RAY DIFFRACTIONr_mcangle_it1.01822914
X-RAY DIFFRACTIONr_scbond_it1.69931030
X-RAY DIFFRACTIONr_scangle_it2.8354.5948
LS refinement shellResolution: 1.58→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 227 -
Rwork0.266 4359 -
all-4586 -
obs--76.26 %

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