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- PDB-7nc7: Crystal structure of fructose-bisphosphate aldolases FBAC from Ba... -

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Basic information

Entry
Database: PDB / ID: 7nc7
TitleCrystal structure of fructose-bisphosphate aldolases FBAC from Bacillus methanolicus
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / glycolytic aldolase
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-1,6-bisphosphate aldolase, class 2 / : / 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-type TIM barrel
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / Putative fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesBacillus methanolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEinsle, O. / Zhang, L. / Guetle, D. / Jacquot, J.P.
CitationJournal: Front Microbiol / Year: 2021
Title: Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference
Authors: Schultenkamper, K. / Gutle, D.D. / Lopez, M.G. / Keller, L.B. / Zhang, L. / Einsle, O. / Jacquot, J.P. / Wendisch, V.F.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8244
Polymers61,4842
Non-polymers3402
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-19 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.970, 98.260, 139.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fructose-bisphosphate aldolase


Mass: 30742.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus (strain MGA3 / ATCC 53907) (bacteria)
Strain: MGA3 / ATCC 53907 / Gene: fbaC, BMMGA3_16125 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3EBM6, fructose-bisphosphate aldolase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→27.42 Å / Num. obs: 24421 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC1/2: 0.996 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 2158 / CC1/2: 0.521

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q94

3q94


Resolution: 2.2→27.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.398 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 946 5.2 %RANDOM
Rwork0.1885 ---
obs0.1919 17198 71.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.81 Å2 / Biso mean: 36.602 Å2 / Biso min: 17.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.2→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 20 150 4275
Biso mean--65.05 36.07 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174130
X-RAY DIFFRACTIONr_angle_refined_deg1.281.6455723
X-RAY DIFFRACTIONr_angle_other_deg1.3621.589563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50123.455191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74615761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9831520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 19 -
Rwork0.269 475 -
all-494 -
obs--26.26 %

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