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- PDB-3mbd: Crystal structure of fructose bisphosphate aldolase from Encephal... -

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Basic information

Entry
Database: PDB / ID: 3mbd
TitleCrystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to phosphate
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / ALDOLASE / Glycolysis / Schiff base / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi.
Authors: Gardberg, A. / Sankaran, B. / Davies, D. / Bhandari, J. / Staker, B. / Stewart, L.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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 / 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 / _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)38,3933
Polymers38,2631
Non-polymers1302
Water3,459192
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7876
Polymers76,5262
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2840 Å2
ΔGint-46 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.960, 137.610, 62.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fructose-bisphosphate aldolase /


Mass: 38263.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU01_0240 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SSM8, fructose-bisphosphate aldolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 90% PACT SCREEN CONDITION F10, 10% ADDITIVE SCREEN G12: 90MM BIS-TRIS PROPANE PH 6.5, 18% PEG 3350, 18 MM NAKHPO4, 10 MM UREA, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→36.8 Å / Num. all: 35792 / Num. obs: 35720 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.83
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO5

1qo5


Resolution: 2→35.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.361 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19021 1749 4.9 %RANDOM
Rwork0.1624 ---
obs0.16375 33882 99.58 %-
all-35792 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 6 192 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222738
X-RAY DIFFRACTIONr_bond_other_d0.0010.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9843704
X-RAY DIFFRACTIONr_angle_other_deg0.91334702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38524.052116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74815516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1251518
X-RAY DIFFRACTIONr_chiral_restr0.090.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.51691
X-RAY DIFFRACTIONr_mcbond_other0.2081.5703
X-RAY DIFFRACTIONr_mcangle_it1.37122728
X-RAY DIFFRACTIONr_scbond_it2.23431047
X-RAY DIFFRACTIONr_scangle_it3.6454.5965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 129 -
Rwork0.214 2444 -
obs--99.19 %
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)
17.62863.39332.57946.91032.92767.28550.3083-0.5179-0.69350.89260.0509-0.63830.55160.3266-0.35920.24080.087-0.07330.12060.05590.1611-0.45-26.8763.888
22.63980.2055-0.82251.56410.29771.9-0.0207-0.1292-0.04020.12690.07650.28530.1236-0.126-0.05580.1392-0.08650.03950.10510.04870.1342-26.029-24.3594.48
30.9919-0.1403-0.05291.9921-0.20571.88520.0323-0.05810.07570.11160.00840.1009-0.042-0.0972-0.04070.0346-0.01760.01790.021-0.0030.0506-12.689-9.844-3.556
41.40730.0798-0.13631.08210.06571.02930.01940.175-0.0092-0.1220.01230.13450.0987-0.1358-0.03170.0664-0.0326-0.02340.05360.00590.0675-13.066-20.47-17.564
52.0792-0.3408-1.90241.4230.9273.2971-0.03270.1006-0.26480.10760.02330.26210.2626-0.26330.00940.1557-0.1394-0.0180.15620.0530.2196-29.764-31.858-6.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 15
2X-RAY DIFFRACTION2A16 - 98
3X-RAY DIFFRACTION3A99 - 183
4X-RAY DIFFRACTION4A184 - 290
5X-RAY DIFFRACTION5A291 - 338

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