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

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Basic information

Entry
Database: PDB / ID: 3tml
TitleCrystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia
Components2-dehydro-3-deoxyphosphooctonate aldolase
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
2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
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_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
B: 2-dehydro-3-deoxyphosphooctonate aldolase
C: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,84914
Polymers125,1314
Non-polymers71810
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2-dehydro-3-deoxyphosphooctonate aldolase
C: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

B: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,84914
Polymers125,1314
Non-polymers71810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area12160 Å2
ΔGint-208 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.380, 149.010, 151.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31282.639 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: kdsA, BceJ2315_21430, BCAL2180 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B4EDA2, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EBS internal tracking number 224146E2. JCSG E2. 2000 mM Ammonium sulfate, cacodylate 6.5, 200 mM NaCl. BuceA.00102.a.A1 PS01142 at 74 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-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→43.26 Å / Num. obs: 85003 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28.944 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.954.10.5642.425066617099.7
1.95-20.4642.824808608699.9
2-2.060.3753.524231594699.9
2.06-2.120.2834.523208568599.9
2.12-2.190.2385.222779556599.9
2.19-2.270.2185.721321528797.7
2.27-2.360.1776.721288521299.8
2.36-2.450.1398.120267498099.8
2.45-2.560.1219.219787483999.9
2.56-2.690.09910.818782461299.8
2.69-2.830.08712.317889440399.9
2.83-30.07115.216912417299.9
3-3.210.05718.515830393599.8
3.21-3.470.04622.514645365999.7
3.47-3.80.04424.213342337099.3
3.8-4.250.03827.412168308999.4
4.25-4.910.03529.810711272999.7
4.91-6.010.03428.39212235399.7
6.01-8.50.03429.37061183599.1
8.50.0330.83839107697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.71 Å
Translation2.5 Å47.71 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T4C

3t4c


Resolution: 1.9→43.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.449 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4254 5 %RANDOM
Rwork0.187 ---
obs0.189 85003 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.089 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---1.25 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7855 0 34 405 8294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198107
X-RAY DIFFRACTIONr_bond_other_d0.0010.025357
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.97311025
X-RAY DIFFRACTIONr_angle_other_deg0.955313115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36951070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66724.036337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.041151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6331555
X-RAY DIFFRACTIONr_chiral_restr0.0790.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021594
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 302 -
Rwork0.298 5467 -
all-5769 -
obs--99.52 %
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)
10.30610.38540.20382.17320.42091.2734-0.03920.01-0.0545-0.1273-0.0135-0.02340.3348-0.04620.05270.2649-0.01050.0270.0034-0.00860.0411-12.623-20.16738.253
20.32660.26990.32971.5038-0.19371.59160.0176-0.0253-0.0470.0936-0.0691-0.07960.59840.06270.05160.43160.01630.03310.01340.01670.0349-11.833-17.248-3.615
30.3303-0.0617-0.32841.3098-0.50861.5349-0.02950.02850.02630.0086-0.001-0.0254-0.26410.00010.03050.232-0.0136-0.03450.01810.00250.049-10.59814.78936.164
40.2473-0.0195-0.04521.11110.2661.9624-0.0422-0.01690.02040.0556-0.03380.022-0.3279-0.07210.0760.20950.0113-0.02070.0143-0.0190.0461-13.95817.582-0.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 283
2X-RAY DIFFRACTION2B0 - 283
3X-RAY DIFFRACTION3C1 - 283
4X-RAY DIFFRACTION4D1 - 283

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