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

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Basic information

Entry
Database: PDB / ID: 4def
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
Function / homology
Function and homology information


cell wall / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / zymogen binding / 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 / Fructose-bisphosphate aldolase / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsCapodagli, G.C. / Pegan, S.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_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_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_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

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4895
Polymers37,2761
Non-polymers2134
Water7,638424
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)149,95620
Polymers149,1044
Non-polymers85116
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 area14750 Å2
ΔGint-385 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.655, 119.708, 164.826
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-620-

HOH

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 26% PEG 300, 0.1 M sodium acetate, 2% DMSO, 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: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→96.9 Å / Num. all: 73747 / Num. obs: 65340 / % possible obs: 88.6 %
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / % possible all: 94.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.34 Å
Translation2.5 Å33.34 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
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: 1.64→33.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.1934 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8653 / SU B: 1.411 / SU ML: 0.048 / SU R Cruickshank DPI: 0.074 / SU Rfree: 0.0723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 3306 5.1 %RANDOM
Rwork0.189 ---
all0.1895 73747 --
obs0.1895 65335 88.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.79 Å2 / Biso mean: 29.4155 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å20 Å2
2---1.42 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.64→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 7 424 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022603
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9533544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1025348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96825.047107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6115420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.802157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211987
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 228 -
Rwork0.282 4592 -
all-4820 -
obs--93.56 %

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