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- PDB-7ncc: Crystal structure of fructose-bisphosphate aldolase FBAP from Bac... -

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Basic information

Entry
Database: PDB / ID: 7ncc
TitleCrystal structure of fructose-bisphosphate aldolase FBAP from Bacillus methanolicus
ComponentsPutative class II fructose-1,6-bisphosphate aldolase
KeywordsLYASE / gluconeogenic aldolase
Function / homology
Function and homology information


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
IMIDAZOLE / D-MALATE / PHOSPHATE ION / Putative class II fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesBacillus methanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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: Putative class II fructose-1,6-bisphosphate aldolase
B: Putative class II fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,79110
Polymers61,0182
Non-polymers7738
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-53 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.582, 122.121, 160.963
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 Putative class II fructose-1,6-bisphosphate aldolase


Mass: 30508.965 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: fba / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6TV43
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 4000, 0.2M imidazole/malate buffer at pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.79 Å / Num. obs: 60641 / % possible obs: 99.3 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 4427 / CC1/2: 0.661

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Processing

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

3q94


Resolution: 2→44.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.569 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 3109 5.1 %RANDOM
Rwork0.1863 ---
obs0.1896 57489 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.39 Å2 / Biso mean: 35.959 Å2 / Biso min: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å2-0 Å20 Å2
2---0.18 Å2-0 Å2
3---1.76 Å2
Refinement stepCycle: final / Resolution: 2→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 44 282 4596
Biso mean--47.25 44.39 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134397
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174246
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.6325939
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5789831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14224.33194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70215780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4521516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_rigid_bond_restr4.69338642
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 259 -
Rwork0.312 4166 -
all-4425 -
obs--99.17 %
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)
10.5499-0.29240.17310.4313-0.5031.0437-0.08360.08830.00770.0025-0.0445-0.0299-0.08170.22280.12820.1017-0.0858-0.02720.12310.04810.02318.190433.293623.7288
20.43810.2127-0.10310.2808-0.48941.3687-0.0517-0.0180.0319-0.0296-0.061-0.02040.08670.16920.11270.09870.04920.01590.06030.02480.016618.405510.546356.9681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B1 - 301

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