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- PDB-3sz8: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase fr... -

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Basic information

Entry
Database: PDB / ID: 3sz8
TitleCrystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
Components2-dehydro-3-deoxyphosphooctonate aldolase 2
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytoplasm
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 2-dehydro-3-deoxyphosphooctonate aldolase 2
B: 2-dehydro-3-deoxyphosphooctonate aldolase 2
C: 2-dehydro-3-deoxyphosphooctonate aldolase 2
D: 2-dehydro-3-deoxyphosphooctonate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1778
Polymers121,9414
Non-polymers2364
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-69 kcal/mol
Surface area36120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.490, 83.320, 87.870
Angle α, β, γ (deg.)90.000, 116.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
2-dehydro-3-deoxyphosphooctonate aldolase 2 / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 2 / KDO-8-phosphate synthase 2 / Phospho-2- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 2 / KDO-8-phosphate synthase 2 / Phospho-2-dehydro-3-deoxyoctonate aldolase 2


Mass: 30485.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: kdsA, kdsA2, BURPS1710b_3264 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3JP68, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS internal tracking number 223672H7. PACT H7. 0.2 M Na acetate, 0.1 M Bis Tris propane pH 8.5, 20% PEG 3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 68845 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.651 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.13.40.472.617312502299.1
2.1-2.160.3873.217591497899.5
2.16-2.220.3044.117092479999.5
2.22-2.290.274.816844468599.2
2.29-2.370.235.516610454799.7
2.37-2.450.1956.516124438099.3
2.45-2.540.1657.615697424899.6
2.54-2.650.1349.315103406699.5
2.65-2.760.11910.514597395299.4
2.76-2.90.09612.713752370599.2
2.9-3.060.0815.113211357299.4
3.06-3.240.06318.412414337099.2
3.24-3.470.0522.711392314899
3.47-3.740.0427.210615295598.7
3.74-4.10.03429.99653271098.7
4.1-4.580.03133.78758245398.3
4.58-5.290.02935.27739215698.4
5.29-6.480.02933.56747185498.8
6.48-9.170.02436.75212143998.6
9.17-500.02140.6285780697.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.52 Å
Translation2.5 Å45.52 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→43.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.166 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3483 5.1 %RANDOM
Rwork0.183 ---
obs0.185 68771 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.9 Å2
2--0.22 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7789 0 16 555 8360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227987
X-RAY DIFFRACTIONr_bond_other_d0.0010.025297
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.97910845
X-RAY DIFFRACTIONr_angle_other_deg0.933313026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00424.481308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.085151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.221541
X-RAY DIFFRACTIONr_chiral_restr0.0820.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021523
X-RAY DIFFRACTIONr_mcbond_it0.7221.55253
X-RAY DIFFRACTIONr_mcbond_other0.1761.52137
X-RAY DIFFRACTIONr_mcangle_it1.32428419
X-RAY DIFFRACTIONr_scbond_it2.17632734
X-RAY DIFFRACTIONr_scangle_it3.624.52419
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 250 -
Rwork0.226 4754 -
all-5004 -
obs--99.07 %
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)
10.8869-0.0712-0.14780.51440.08480.7484-0.0145-0.0429-0.0172-0.01860.0257-0.038-0.0420.0803-0.01120.0091-0.01750.01340.0444-0.01330.08175.30632.469100.491
20.85890.01720.22540.46060.1260.5017-0.0005-0.09680.0088-0.0143-0.0014-0.02-0.0055-0.00140.00190.0432-0.0060.01350.0456-0.01320.0395-25.38137.41116.779
31.03310.29690.12370.5422-0.05440.5748-0.02730.1453-0.0693-0.04460.0444-0.0172-0.02370.0329-0.01720.0668-0.01390.0390.0752-0.02740.0296-13.54429.11468.241
40.50920.1288-0.16920.5215-0.03731.0574-0.00470.0531-0.0092-0.03760.0161-0.02020.0197-0.0489-0.01140.035-0.0062-0.00760.0265-0.01420.0634-42.86524.50286.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 278
2X-RAY DIFFRACTION2B0 - 279
3X-RAY DIFFRACTION3C1 - 279
4X-RAY DIFFRACTION4D0 - 279

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