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

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Basic information

Entry
Database: PDB / ID: 3qrh
TitleCrystal structure of fructose bisphosphate aldolase from Encephalitozoon Cuniculi, bound to glyceraldehyde 3-phosphate
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / SSGCID / Encephalitozoon Cuniculi / aldolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
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
GLYCERALDEHYDE-3-PHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of fructose bisphosphate aldolase from Encephalitozoon Cuniculi, bound to glyceraldehyde 3-phosphate
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A. / Arakaki, T. / Staker, B.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)38,4332
Polymers38,2631
Non-polymers1701
Water3,981221
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8664
Polymers76,5262
Non-polymers3402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.540, 138.090, 62.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

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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-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG6000, 0.1 M HEPES, protein at ~22 mg/ml, glyceraldehyde 3-phosphate at 10 mM., pH 7.0, 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 315 / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36410 / Num. obs: 36353 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 35.215 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.64
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2-2.056.10.4384.21619026502650100
2.05-2.110.3625.215769260199.8
2.11-2.170.2596.915369250399.9
2.17-2.240.228.1149802449100
2.24-2.310.1919.614284238899.9
2.31-2.390.14911.8139762277100
2.39-2.480.12114.3136812236100
2.48-2.580.09817.213016213599.9
2.58-2.70.08419.4124672053100
2.7-2.830.06822.812033198199.9
2.83-2.980.05727.2114411882100
2.98-3.160.0493110768178099.9
3.16-3.380.0437.8101061689100
3.38-3.650.03641.991231545100
3.65-40.033478606147099.8
4-4.470.028527605131199.8
4.47-5.160.025546776117099.8
5.16-6.320.02552.1596599899.9
6.32-8.940.02255.7467379199.5
8.940.01958.8241944494.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.58 Å
Translation2.5 Å19.58 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3MBF
Resolution: 2→46.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.312 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1783 4.9 %RANDOM
Rwork0.163 ---
obs0.164 36267 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.407 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 2→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 9 221 2821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222672
X-RAY DIFFRACTIONr_bond_other_d0.0010.021826
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9833617
X-RAY DIFFRACTIONr_angle_other_deg0.91934468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46324.22109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1171515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_mcbond_it0.7641.51678
X-RAY DIFFRACTIONr_mcbond_other0.2241.5699
X-RAY DIFFRACTIONr_mcangle_it1.34322689
X-RAY DIFFRACTIONr_scbond_it2.1863994
X-RAY DIFFRACTIONr_scangle_it3.4824.5923
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 128 -
Rwork0.206 2514 -
all-2642 -
obs-2650 99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6097-0.33370.78680.96740.09581.1170.02320.158-0.0377-0.19860.02890.1758-0.1873-0.094-0.05210.10610.0517-0.02830.08830.0250.0469-22.355724.6332-4.3009
20.57340.23830.13711.51080.02461.20580.03880.057-0.1656-0.1030.0277-0.03280.0903-0.0821-0.06650.04110.0161-0.01750.0379-0.01240.0574-12.47179.33233.0711
31.20370.07170.24390.82350.20551.03920.0416-0.1482-0.09570.06820.03560.0234-0.062-0.139-0.07710.03520.02430.01040.04670.02560.0389-13.345820.463817.1647
41.07690.18631.10031.19640.52342.02690.0139-0.11560.1035-0.1142-0.01360.2532-0.2889-0.4021-0.00030.12180.1190.01420.15390.03380.1271-30.399332.13556.8547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 99
2X-RAY DIFFRACTION2A100 - 177
3X-RAY DIFFRACTION3A178 - 292
4X-RAY DIFFRACTION4A293 - 338

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