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- PDB-2opi: Crystal Structure of L-fuculose-1-phosphate aldolase from Bactero... -

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Basic information

Entry
Database: PDB / ID: 2opi
TitleCrystal Structure of L-fuculose-1-phosphate aldolase from Bacteroides thetaiotaomicron
ComponentsL-fuculose-1-phosphate aldolase
KeywordsLYASE / Bacteroides thetaiotaomicron / L-fuculose-1-phosphate aldolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity
Similarity search - Function
L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Class II aldolase/adducin family protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsChang, C. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of L-fuculose-1-phosphate aldolase from Bacteroides thetaiotaomicron
Authors: Chang, C. / Volkart, L. / Abdullah, J. / Joachimiak, A.
History
DepositionJan 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-fuculose-1-phosphate aldolase
B: L-fuculose-1-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5584
Polymers47,3662
Non-polymers1922
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L-fuculose-1-phosphate aldolase
B: L-fuculose-1-phosphate aldolase
hetero molecules

A: L-fuculose-1-phosphate aldolase
B: L-fuculose-1-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1178
Polymers94,7334
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area9640 Å2
ΔGint-138 kcal/mol
Surface area31570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.934, 115.934, 73.722
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein L-fuculose-1-phosphate aldolase


Mass: 23683.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: fucA, BT_1274 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q9RQ12, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 20166 / Num. obs: 19838 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 23.81
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 1.67 / Num. unique all: 1835 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.55 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.416 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25955 1002 5.1 %RANDOM
Rwork0.22499 ---
all0.22667 18536 --
obs0.22667 18536 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 10 40 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9634422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.73224.672137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33515548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5931514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022436
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21523
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7571.52106
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98723329
X-RAY DIFFRACTIONr_scbond_it1.51831291
X-RAY DIFFRACTIONr_scangle_it2.314.51093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 74 -
Rwork0.3 1246 -
obs--90.85 %
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)
19.62-2.1419-3.3516.43610.36374.6237-0.1020.0760.0219-0.06630.1828-0.63330.02770.5276-0.0808-0.1679-0.069-0.0167-0.044-0.0408-0.036225.56184.54312.934
21.232-0.2608-0.49282.05160.23440.80670.0215-0.0352-0.0096-0.18910.0163-0.1575-0.11760.0529-0.0378-0.0926-0.00130.0317-0.1326-0.0097-0.121113.30780.9138.252
31.27750.3154-0.57470.6882-0.13611.0503-0.1240.1869-0.1548-0.06340.0143-0.00790.1472-0.03970.1096-0.07450.01610.0051-0.1207-0.0189-0.10047.79677.9427.365
42.3137-1.99020.62793.928-0.13790.80080.06540.12510.3254-0.3696-0.1214-0.0709-0.3375-0.09160.05610.00720.0193-0.0277-0.18350.0129-0.15252.8997.7825.62
510.0053-5.02933.1214.52780.98494.2347-0.7411-0.49060.47271.66890.3852-0.6299-0.41710.95240.35590.2094-0.0243-0.09060.04730.08590.114825.57588.71440.4
63.6707-0.222-0.42391.069-0.33920.7447-0.0067-0.3139-0.16790.571-0.0663-0.13180.06130.06550.0730.09020.0045-0.0826-0.1860.0308-0.128914.92783.96544.602
71.8645-0.4177-0.12661.63370.481.0956-0.2011-0.2278-0.10240.52790.0696-0.1301-0.03730.03370.13160.08530.0025-0.0457-0.14550.0314-0.1837.9483.19946.891
82.0338-0.54690.46812.04340.75582.7505-0.04970.0988-0.12040.1817-0.00890.13880.08880.04460.0585-0.1008-0.03010.0267-0.18270.0314-0.13763.27581.20827.032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION1AA45 - 5445 - 54
3X-RAY DIFFRACTION2AA22 - 4422 - 44
4X-RAY DIFFRACTION2AA55 - 6755 - 67
5X-RAY DIFFRACTION2AA87 - 9787 - 97
6X-RAY DIFFRACTION2AA125 - 132125 - 132
7X-RAY DIFFRACTION2AA150 - 165150 - 165
8X-RAY DIFFRACTION3AA68 - 8668 - 86
9X-RAY DIFFRACTION3AA98 - 10698 - 106
10X-RAY DIFFRACTION3AA133 - 149133 - 149
11X-RAY DIFFRACTION4AA107 - 124107 - 124
12X-RAY DIFFRACTION4AA166 - 203166 - 203
13X-RAY DIFFRACTION5BB1 - 211 - 21
14X-RAY DIFFRACTION5BB45 - 5445 - 54
15X-RAY DIFFRACTION6BB22 - 4422 - 44
16X-RAY DIFFRACTION6BB55 - 6755 - 67
17X-RAY DIFFRACTION6BB87 - 9787 - 97
18X-RAY DIFFRACTION6BB125 - 132125 - 132
19X-RAY DIFFRACTION6BB159 - 165159 - 165
20X-RAY DIFFRACTION7BB68 - 8668 - 86
21X-RAY DIFFRACTION7BB98 - 10698 - 106
22X-RAY DIFFRACTION7BB133 - 149133 - 149
23X-RAY DIFFRACTION8BB107 - 124107 - 124
24X-RAY DIFFRACTION8BB166 - 203166 - 203

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