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- PDB-3tmq: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 3tmq
TitleCrystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei in complex with D-arabinose-5-phosphate
Components2-dehydro-3-deoxyphosphooctonate aldolase 2
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / aldolase barrel
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
ARABINOSE-5-PHOSPHATE / NITRATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 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)123,33521
Polymers121,9414
Non-polymers1,39517
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18890 Å2
ΔGint-25 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.720, 92.080, 152.980
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 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-A5P / ARABINOSE-5-PHOSPHATE


Mass: 232.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O8P
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number224822. PACT screen F5. 0.2M Sodium nitrate, 0.1M BIS-TRIS propane, 20% PEG3350, protein drop contains 10mM D-arabinose-5-phosphate. BupsA.00102a.A1 PS00621 30.3mg/ml. ...Details: Internal tracking number224822. PACT screen F5. 0.2M Sodium nitrate, 0.1M BIS-TRIS propane, 20% PEG3350, protein drop contains 10mM D-arabinose-5-phosphate. BupsA.00102a.A1 PS00621 30.3mg/ml., pH 6.5, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→49.2 Å / Num. all: 80219 / Num. obs: 78647 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.32 % / Biso Wilson estimate: 26.74 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.14.310.5533.122158514387.7
2.1-2.160.465426859543195.7
2.16-2.220.3815.130723555399.4
2.22-2.290.32629803538799.4
2.29-2.370.2966.528927518999.3
2.37-2.450.2477.628031504299.8
2.45-2.540.2118.927238490199.8
2.54-2.650.16710.6262664738100
2.65-2.760.1511.724996450999.8
2.76-2.90.12513.524053434999.8
2.9-3.060.10715.822612412999.7
3.06-3.240.08618.921123388999.5
3.24-3.470.06922.219625369899.4
3.47-3.740.05726.217936340998.8
3.74-4.10.05228.216342313398.6
4.1-4.580.04430.314568286798.5
4.58-5.290.04231.412947251597.6
5.29-6.480.04329.911340215497.7
6.48-9.170.035338717167996
9.170.03133.8443593290.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.99 Å
Translation2.5 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
MD2data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZ8

3sz8


Resolution: 2.1→49.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.273 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3679 5 %RANDOM
Rwork0.179 ---
obs0.181 73746 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--2.19 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 88 629 8761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198272
X-RAY DIFFRACTIONr_bond_other_d0.0010.025487
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.98411212
X-RAY DIFFRACTIONr_angle_other_deg1.122313452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91851091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55723.824306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.906151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2161549
X-RAY DIFFRACTIONr_chiral_restr0.0770.21325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021598
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 214 -
Rwork0.219 4663 -
all-4877 -
obs--94.75 %
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)
10.4705-0.1041-0.08650.379-0.06270.80460.0062-0.09880.08480.0501-0.0001-0.0022-0.19090.0958-0.00610.0643-0.03530.00380.0842-0.05090.038672.902168.797718.1549
20.692-0.20270.12580.68470.2870.68580.0084-0.0794-0.09260.06290.02020.02840.11910.0708-0.02850.0390.00550.00920.09550.0310.032771.439934.29626.0705
30.5440.0806-0.06820.3716-0.02590.76420.01510.04350.035-0.04440.0010.0105-0.0750.0348-0.01610.0253-0.0083-0.00150.0573-0.01540.011474.382360.7784-14.8027
40.58330.0920.27411.0353-0.39720.6250.0290.013-0.1087-0.07170.02480.07870.0992-0.0032-0.05380.02840.0034-0.02690.0477-0.03420.085562.712528.0962-7.337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 280
2X-RAY DIFFRACTION2B0 - 281
3X-RAY DIFFRACTION3C0 - 280
4X-RAY DIFFRACTION4D1 - 281

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