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- PDB-3t4c: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase fr... -

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Basic information

Entry
Database: PDB / ID: 3t4c
TitleCrystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria
Components2-dehydro-3-deoxyphosphooctonate aldolase 1
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 ambifaria (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.95 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 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 1
B: 2-dehydro-3-deoxyphosphooctonate aldolase 1
C: 2-dehydro-3-deoxyphosphooctonate aldolase 1
D: 2-dehydro-3-deoxyphosphooctonate aldolase 1


Theoretical massNumber of molelcules
Total (without water)125,0634
Polymers125,0634
Non-polymers00
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-63 kcal/mol
Surface area35860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.130, 129.500, 169.390
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 1 / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 1 / KDO-8-phosphate synthase 1 / Phospho-2- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 1 / KDO-8-phosphate synthase 1 / Phospho-2-dehydro-3-deoxyoctonate aldolase 1


Mass: 31265.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: kdsA1, BamMC406_2018 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1YT10, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS internal tracking number 224045c2 WIZARD 3/4 C2. 24%(w/v) PEG 1500, 20%(v/v) Glycerol, BuamA.00102.a.A1 PS01117 at 74 mg/mL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→45.94 Å / Num. obs: 79104 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 30.992 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-22.80.4012.414575522889.8
2-2.060.343.218819561498.1
2.06-2.120.2824.723720550199.7
2.12-2.180.2676.4318835379100
2.18-2.250.2437.7361845214100
2.25-2.330.2198.4352745063100
2.33-2.420.1829.833829485299.9
2.42-2.520.16510.832844470099.9
2.52-2.630.14112.131204449499.7
2.63-2.760.1313.230399435999.8
2.76-2.910.10715.428300409699.7
2.91-3.080.09617.126712392999.8
3.08-3.30.0851924641365499.7
3.3-3.560.07322.222743343799.6
3.56-3.90.06623.520384312999.6
3.9-4.360.05925.419015290899.6
4.36-5.030.05826.116776256699.7
5.03-6.170.05425.614975222099.8
6.17-8.720.04526.211727173499.8
8.720.03627.26407102797.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.94 Å
Translation2.5 Å45.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: 3SZ8

3sz8


Resolution: 1.95→44.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.168 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3951 5 %RANDOM
Rwork0.17 ---
obs0.172 78773 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7890 0 0 561 8451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198164
X-RAY DIFFRACTIONr_bond_other_d0.0010.025437
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.96911102
X-RAY DIFFRACTIONr_angle_other_deg0.969313327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00324.345359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.701151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1761554
X-RAY DIFFRACTIONr_chiral_restr0.0920.21293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021593
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 246 -
Rwork0.246 4751 -
all-4997 -
obs--89.28 %
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)
12.2583-1.02630.24361.2969-0.66823.1607-0.0702-0.1731-0.06770.2774-0.046-0.0156-0.06810.26490.11620.151-0.0499-0.02390.1860.00380.014446.141133.79897.818
20.5072-0.03050.270.641-0.17342.1102-0.0028-0.1023-0.00950.07440.07090.06510.0324-0.2075-0.06810.091-0.01710.0110.16010.01730.063730.415130.48685.975
31.6303-0.1560.52520.7776-1.2812.56420.0190.0356-0.04460.0655-0.1128-0.073-0.20340.38030.09380.1234-0.0685-0.03450.1520.00310.062847.428140.35782.68
41.7219-0.4587-0.5630.7412-0.40182.7999-0.0060.07660.0329-0.1374-0.0593-0.01180.07920.39940.06530.16840.0067-0.00390.18220.02220.003738.933122.62430.469
50.40220.05490.39240.24710.25732.00340.01610.0290.069-0.0813-0.02220.035-0.33280.07630.00610.18620.0046-0.0110.110.03190.068529.724133.57143.659
61.3669-0.4527-0.08010.4438-0.04881.83130.0245-0.0111-0.0478-0.0666-0.0484-0.00150.27360.30990.02390.1650.0502-0.00040.14330.01040.031136.075114.48845.586
72.67190.3607-1.55360.701-1.4063.11170.0277-0.0835-0.0372-0.1230.20860.12320.2295-0.3323-0.23630.1347-0.0572-0.06060.11980.05990.13614.566101.63769.005
80.28050.09950.05411.3371-0.67250.88020.0283-0.0978-0.02640.0497-0.04120.0083-0.00770.06990.01290.0995-0.0086-0.00270.14210.03560.078631.656109.71273.862
91.46820.06660.02770.9959-0.8961.47960.0529-0.00930.0631-0.0940.09260.18260.1113-0.1794-0.14550.1087-0.0308-0.02760.1130.03120.098119.429112.70758.029
100.572-1.2238-0.13374.4216-1.68292.19220.15590.087-0.0014-0.179-0.2569-0.0755-0.25360.08060.1010.1966-0.089-0.02220.1410.0320.102842.453161.50155.776
110.18680.04710.24261.7326-0.12571.0470.03780.0290.0412-0.1948-0.0908-0.1998-0.03070.23340.05310.1117-0.03520.03920.17910.0310.09148.614144.90756.855
120.9233-0.3881-0.08042.784-1.54541.97340.00480.05150.09780.2290.05880.2363-0.3587-0.0379-0.06360.1587-0.03390.00410.0660.00920.094137.386153.970.659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION2A89 - 200
3X-RAY DIFFRACTION3A201 - 281
4X-RAY DIFFRACTION4B1 - 103
5X-RAY DIFFRACTION5B104 - 198
6X-RAY DIFFRACTION6B199 - 281
7X-RAY DIFFRACTION7C1 - 83
8X-RAY DIFFRACTION8C84 - 198
9X-RAY DIFFRACTION9C199 - 281
10X-RAY DIFFRACTION10D1 - 116
11X-RAY DIFFRACTION11D117 - 198
12X-RAY DIFFRACTION12D199 - 281

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