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- PDB-6mdy: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 6mdy
TitleCrystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsHYDROLASE / NIAID / structural genomics / aldolase / phosphoenolpyruvate / D-arabinose 5-phosphate / 3-deoxy-D-manno-octulosonate 8-phosphate / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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


Theoretical massNumber of molelcules
Total (without water)124,1914
Polymers124,1914
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-55 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.520, 87.320, 160.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 36 or (resid 37...
21(chain B and ((resid 0 and (name N or name...
31(chain C and (resid 0 through 22 or (resid 23...
41(chain D and (resid 0 through 1 or (resid 2...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEU(chain A and (resid 0 through 36 or (resid 37...AA0 - 368 - 44
12LYSLYSGLUGLU(chain A and (resid 0 through 36 or (resid 37...AA37 - 3845 - 46
13HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
14HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
15HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
16HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
21HISHISHISHIS(chain B and ((resid 0 and (name N or name...BB08
22HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
23HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
24HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
25HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
31HISHISVALVAL(chain C and (resid 0 through 22 or (resid 23...CC0 - 228 - 30
32ILEILEGLUGLU(chain C and (resid 0 through 22 or (resid 23...CC23 - 2431 - 32
33HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
34HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
35HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
36HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
41HISHISMETMET(chain D and (resid 0 through 1 or (resid 2...DD0 - 18 - 9
42ARGARGARGARG(chain D and (resid 0 through 1 or (resid 2...DD210
43HISHISPHEPHE(chain D and (resid 0 through 1 or (resid 2...DD-1 - 2747 - 282

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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 / KDOPS / Phospho- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho-2-dehydro-3-deoxyoctonate aldolase


Mass: 31047.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: kdsA, lpg1182 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZWA3, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: LepnA.00102.a.B1.PS38404 at 22.83 mg/mL against JCSG+ screen condition H3 25% PEG 3350, 0.1 M BisTris pH 5.5, supplemented with 15% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: LepnA.00102.a.B1.PS38404 at 22.83 mg/mL against JCSG+ screen condition H3 25% PEG 3350, 0.1 M BisTris pH 5.5, supplemented with 15% ethylene glycol as cryo-protectant, crystal tracking ID 298231h3, unique puck ID uya9-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98782 Å / Relative weight: 1
ReflectionResolution: 2.55→45.554 Å / Num. obs: 33563 / % possible obs: 99.9 % / Redundancy: 6.166 % / Biso Wilson estimate: 44.776 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.098 / Χ2: 1.003 / Net I/σ(I): 17.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.626.2850.5773.2724150.8750.631100
2.62-2.696.2640.5213.6123880.8950.569100
2.69-2.776.2450.4184.3923210.9160.456100
2.77-2.856.2650.355.3722390.9430.382100
2.85-2.946.2780.2936.3221810.960.3299.9
2.94-3.056.2480.2527.2421470.9690.275100
3.05-3.166.2340.1989.2920290.9790.216100
3.16-3.296.2360.15811.5219650.9860.173100
3.29-3.446.2040.12114.7419100.9910.13299.9
3.44-3.616.2110.08520.0318020.9960.093100
3.61-3.86.1940.07222.7917460.9970.07999.9
3.8-4.036.1710.05927.1616360.9980.065100
4.03-4.316.1620.0473315510.9980.052100
4.31-4.666.1180.04236.5814550.9990.046100
4.66-5.16.0760.03938.7313430.9990.043100
5.1-5.76.0490.0436.2612090.9990.044100
5.7-6.585.9560.04732.511020.9990.052100
6.58-8.065.8420.03239.3194110.035100
8.06-11.45.6490.02153.474110.023100
11.4-45.5544.8940.02348.814420.9990.02696.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3219)refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TML

3tml


Resolution: 2.55→45.554 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.96
RfactorNum. reflection% reflection
Rfree0.2269 1903 5.68 %
Rwork0.176 --
obs0.1788 33490 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 48.3604 Å2 / Biso min: 17.47 Å2
Refinement stepCycle: final / Resolution: 2.55→45.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 0 140 7412
Biso mean---35.62 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067445
X-RAY DIFFRACTIONf_angle_d0.88110106
X-RAY DIFFRACTIONf_dihedral_angle_d6.635725
X-RAY DIFFRACTIONf_chiral_restr0.0531183
X-RAY DIFFRACTIONf_plane_restr0.0061291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2724X-RAY DIFFRACTION6.133TORSIONAL
12B2724X-RAY DIFFRACTION6.133TORSIONAL
13C2724X-RAY DIFFRACTION6.133TORSIONAL
14D2724X-RAY DIFFRACTION6.133TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5499-2.61360.33231290.234921932322100
2.6136-2.68430.33411330.221622182351100
2.6843-2.76330.29731310.208522482379100
2.7633-2.85250.26671420.203722092351100
2.8525-2.95440.30181380.203122062344100
2.9544-3.07270.2371330.209322352368100
3.0727-3.21250.27541590.196722362395100
3.2125-3.38180.26091500.187722192369100
3.3818-3.59360.21041250.176722542379100
3.5936-3.87090.21141280.16622612389100
3.8709-4.26020.21271200.152522922412100
4.2602-4.87610.17181350.133522812416100
4.8761-6.14090.19441460.155923082454100
6.1409-45.56120.19221340.18192427256199
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)
13.24070.15660.34272.15250.03061.0386-0.05320.73110.0173-0.62910.0652-0.2285-0.05940.268-0.01540.4655-0.01060.04450.4631-0.09640.30590.0035-10.1893-8.025
21.88310.2395-0.10742.1666-0.05393.61330.02650.2268-0.1827-0.3641-0.06230.43340.34820.08970.03610.24430.0196-0.02930.2388-0.03640.311-12.5535-12.63934.1055
34.1816-0.31610.63850.99590.03184.6981-0.10210.23130.1346-0.25090.1568-0.2745-0.15480.1714-0.08440.28710.0130.05080.2745-0.04870.31813.7007-13.35758.7375
44.50092.7322-1.28817.6748-0.52946.60440.014-0.3391-0.35830.5769-0.11970.31360.54280.01970.15060.38540.0988-0.02140.28330.07820.3207-3.3066-23.701937.8069
51.9506-0.538-0.22442.96480.31444.2388-0.1136-0.496-0.21380.79760.06220.00080.5657-0.3144-0.0710.4731-0.08270.01550.46150.07180.2766-10.6391-18.219248.4547
63.1777-0.17130.08763.0655-0.92615.6806-0.0515-0.2270.12960.3059-0.00560.0541-0.3026-0.0193-0.03970.28920.0105-0.03350.3046-0.01720.2121-8.1817-5.998440.5026
71.61760.15150.38121.2767-0.94344.84570.0871-0.240.17650.2256-0.04810.0284-0.0855-0.04230.03180.24310.0167-0.01790.19690.01750.2591-4.7135-4.06229.3509
81.9674-1.2950.04032.0061-1.16034.86760.0274-0.3817-0.4643-0.40780.01470.62520.2665-0.9278-0.01810.3084-0.0249-0.02930.36450.08920.3986-8.4943-15.366126.0498
91.88791.55360.90913.88771.64013.4740.0298-0.3457-0.5870.28330.05050.45970.388-0.3435-0.06770.28040.01520.0010.32930.08740.4431-6.9041-20.753225.3116
103.88223.6681-4.89893.9451-4.6037.61740.1184-0.21870.22340.58630.0356-0.22860.01590.5386-0.16270.33360.0487-0.01520.3286-0.0350.49413.8494-22.425423.5074
113.62061.36012.61612.8308-0.0626.439-0.0602-0.66760.39320.5251-0.05340.1457-0.723-0.44620.04230.53240.18920.11870.5624-0.03180.3348-32.242817.72941.2656
122.45980.2106-0.61151.0214-0.15374.0608-0.0978-0.6321-0.31690.33090.13920.05830.2296-0.1255-0.10450.3410.07220.02160.42450.10420.3109-28.98671.505635.4901
133.26330.3138-0.4017.0605-0.74735.69160.0124-0.38440.1060.38360.2323-0.1455-0.4328-0.1693-0.26680.32510.10520.05140.33660.0050.2533-31.598816.468225.4873
142.9087-1.22410.38762.4880.69573.86180.10390.4194-0.17440.007-0.06790.1440.2160.11840.02510.23540.0402-0.0170.33440.03160.3002-34.9812.7325-5.799
151.3215-0.2370.14691.8334-0.12452.37420.05340.26380.0039-0.2288-0.027-0.1910.05880.2072-0.03730.22250.01190.03730.25610.01010.2793-21.61219.8972-4.6515
166.10190.5862-0.16953.25630.18265.8868-0.0026-0.0294-0.364-0.01110.1520.164-0.022-0.2906-0.11080.2260.0318-0.00380.24250.05940.2493-35.076612.86747.7831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 139 )A0 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 185 )A140 - 185
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 274 )A186 - 274
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 68 )B0 - 68
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 101 )B69 - 101
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 139 )B102 - 139
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 185 )B140 - 185
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 212 )B186 - 212
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 249 )B213 - 249
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 274 )B250 - 274
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 82 )C0 - 82
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 185 )C83 - 185
13X-RAY DIFFRACTION13chain 'C' and (resid 186 through 274 )C186 - 274
14X-RAY DIFFRACTION14chain 'D' and (resid -1 through 60 )D-1 - 60
15X-RAY DIFFRACTION15chain 'D' and (resid 61 through 185 )D61 - 185
16X-RAY DIFFRACTION16chain 'D' and (resid 186 through 274 )D186 - 274

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