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- PDB-6bng: Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acine... -

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Basic information

Entry
Database: PDB / ID: 6bng
TitleStructure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acinetobacter baumannii
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / SSGCID / Acinetobacter baumannii / 2-dehydro-3-deoxyphosphooctonate aldolase / aldolase / kdsA / 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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acinetobacter baumannii
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7116
Polymers64,3262
Non-polymers3844
Water2,846158
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)129,42112
Polymers128,6534
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15470 Å2
ΔGint-185 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.690, 83.930, 87.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-524-

HOH

31B-425-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 6 or (resid 7...
21(chain B and (resid 5 through 13 or (resid 14...

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
11LYSLYSPROPRO(chain A and (resid 5 through 6 or (resid 7...AA5 - 69 - 10
12GLNGLNGLNGLN(chain A and (resid 5 through 6 or (resid 7...AA711
13HISHISSO4SO4(chain A and (resid 5 through 6 or (resid 7...AA - D3 - 3017
14HISHISSO4SO4(chain A and (resid 5 through 6 or (resid 7...AA - D3 - 3017
15HISHISSO4SO4(chain A and (resid 5 through 6 or (resid 7...AA - D3 - 3017
16HISHISSO4SO4(chain A and (resid 5 through 6 or (resid 7...AA - D3 - 3017
21LYSLYSGLYGLY(chain B and (resid 5 through 13 or (resid 14...BB5 - 139 - 17
22ASPASPASPASP(chain B and (resid 5 through 13 or (resid 14...BB1418
23LYSLYSSO4SO4(chain B and (resid 5 through 13 or (resid 14...BB - F5 - 3019
24LYSLYSSO4SO4(chain B and (resid 5 through 13 or (resid 14...BB - F5 - 3019
25LYSLYSSO4SO4(chain B and (resid 5 through 13 or (resid 14...BB - F5 - 3019
26LYSLYSSO4SO4(chain B and (resid 5 through 13 or (resid 14...BB - F5 - 3019

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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: 32163.150 Da / Num. of mol.: 2 / Fragment: AcbaC.18885.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AB307-0294) (bacteria)
Strain: AB307-0294 / Gene: kdsA, ABBFA_001556 / Plasmid: AcbaC.00102.a.B3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: B7H226, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic/Anatrace MCSG-1 screen condition F9:, 30% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate, 50mM BisTris/HCl pH 6.5: AcbaC.00102.a.B3.PS38194 at 23.46mg/ml: cryo: 20% EG: ...Details: Microlytic/Anatrace MCSG-1 screen condition F9:, 30% pentaerythriol ethoxylate 15/4, 50mM Ammonium sulfate, 50mM BisTris/HCl pH 6.5: AcbaC.00102.a.B3.PS38194 at 23.46mg/ml: cryo: 20% EG: tray 289078 F8: puck MKN8-4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 22, 2017
RadiationMonochromator: C[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→47.801 Å / Num. obs: 29750 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.89 % / Biso Wilson estimate: 40.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.077 / Χ2: 1.031 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.264.9570.5052.9621690.9220.564100
2.26-2.324.9790.4613.3120980.9170.515100
2.32-2.394.9810.3784.0220530.9470.422100
2.39-2.464.9770.3334.5819940.9590.37199.9
2.46-2.544.9650.2316.2119400.9820.25899.9
2.54-2.634.9680.2096.7918870.9820.233100
2.63-2.734.9520.1718.1418120.9880.19100
2.73-2.844.9440.1429.5717550.990.159100
2.84-2.974.9340.10612.416740.9940.118100
2.97-3.114.920.08814.3916290.9950.09899.9
3.11-3.284.9010.07417.3315310.9960.08399.9
3.28-3.484.8920.0620.8214490.9970.06799.7
3.48-3.724.850.05224.2313800.9970.058100
3.72-4.024.8160.04826.1912900.9970.05499.9
4.02-4.44.7970.04428.2211850.9980.04999.8
4.4-4.924.7570.04429.8810760.9970.049100
4.92-5.684.7220.04229.69630.9980.04799.9
5.68-6.964.6820.04328.868270.9970.04899.8
6.96-9.844.4920.04230.266600.9950.04799.5
9.84-47.8013.9920.03630.173780.9970.04296.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2947refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lu0

4lu0


Resolution: 2.2→47.801 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1967 6.62 %0
Rwork0.1796 ---
obs0.1828 29722 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.39 Å2 / Biso mean: 63.3913 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 2.2→47.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 20 160 4297
Biso mean--80.25 46.42 -
Num. residues----547
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2351X-RAY DIFFRACTION6.649TORSIONAL
12B2351X-RAY DIFFRACTION6.649TORSIONAL
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 (%)
2.2-2.2550.32841570.258419152072100
2.255-2.3160.28061560.244519272083100
2.316-2.38410.25891520.224819482100100
2.3841-2.46110.25141250.212419612086100
2.4611-2.5490.22061430.190819652108100
2.549-2.65110.25781450.187319402085100
2.6511-2.77170.26191420.187419702112100
2.7717-2.91790.21471170.192819892106100
2.9179-3.10060.26971410.212419802121100
3.1006-3.340.2721320.197919842116100
3.34-3.6760.22231410.174919982139100
3.676-4.20760.19171390.163720102149100
4.2076-5.30010.20221280.142720422170100
5.3001-47.81180.20451490.17082126227599
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)
13.37760.98390.48281.13370.46071.3554-0.1366-0.2772-0.41880.04150.09130.31610.1309-0.18550.01860.30170.02810.07610.31890.11940.568218.5492-11.56926.8857
23.48741.82420.01853.9247-0.36071.8502-0.0256-0.91480.21510.50680.0330.5731-0.0174-0.2280.03950.34280.13690.12730.5078-0.03310.515519.3916-0.830117.6741
33.44090.91590.60462.10370.13931.544-0.1911-0.7255-0.32460.08820.1510.07220.1538-0.11680.05860.29320.08960.04210.33810.1340.466229.4606-7.728213.3065
42.90971.24640.20661.04140.29842.0002-0.1434-0.0316-0.2892-0.09650.14540.0730.1331-0.05690.01040.28350.01640.03630.19320.03790.455131.203-10.4999-1.3559
53.9874-0.1942-1.17272.8791.32583.3226-0.33730.1284-0.0644-0.34560.09260.17250.0029-0.11050.26350.2766-0.0403-0.01630.26480.07170.563615.7095-9.7585-5.3754
60.9174-0.0152-0.11760.3417-0.54240.8953-0.11560.7141-0.4281-0.60630.4876-0.0750.2453-0.4586-0.04610.9225-0.5157-0.07291.2873-0.21560.686618.7337-13.3437-34.3813
70.7767-0.03880.07810.82790.11171.7563-0.23110.5364-0.6392-0.57770.2707-0.14130.4360.1332-0.13751.2463-0.53480.14661.1602-0.58321.060624.2307-28.527-36.2187
80.8050.1097-0.2730.0375-0.15260.7963-0.09310.5932-0.3956-0.4330.00610.12010.4226-0.0904-0.40161.2448-0.62550.10031.56-0.58890.684132.9261-17.7824-42.5542
90.4319-0.0994-0.36610.9534-0.56181.4417-0.1040.5914-0.0934-0.40870.06940.17950.1242-0.0435-0.06421.1786-0.57110.02841.655-0.28090.521528.7077-10.0571-45.8359
100.7101-0.11340.420.44830.12061.1347-0.22381.18110.0377-0.81130.15330.43070.088-0.21990.10.9429-0.4375-0.17721.3126-0.02630.369728.9093-2.1977-37.5111
110.0595-0.11630.54920.2271-1.06636.1156-0.33651.08460.4447-0.66950.14670.3827-0.5632-0.5250.20670.8229-0.2688-0.22281.06140.26570.500624.05075.5418-31.192
120.03190.1185-0.07871.0740.65031.7584-0.29671.11290.2158-0.76440.2420.26840.2952-0.35570.00480.6366-0.249-0.06280.72550.01070.412930.4162-4.5524-25.9747
132.62330.52950.57053.166-0.31473.2515-0.26240.9283-0.3368-0.67110.2749-0.09060.0479-0.05590.00630.5118-0.2503-0.02190.7125-0.08330.479925.7041-7.7213-23.9282
143.7726-0.8663-0.93792.02840.37224.0966-0.29190.6512-0.8042-0.660.3307-0.13560.45-0.07640.00320.5674-0.25950.09460.5863-0.18080.604625.7443-16.9711-22.1779
153.2594-2.3319-2.14232.31051.0581.7568-0.4890.9515-0.741-0.8615-0.04110.06620.4296-0.08180.55011.1688-0.22440.23951.1827-0.37451.164837.3854-24.2574-29.8946
161.5559-2.2667-0.87645.44992.82624.2052-0.40570.5587-0.2879-0.52420.4204-0.40380.3098-0.5460.08610.6685-0.3620.06990.6213-0.14870.786216.302-17.9747-19.8002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 69 )A3 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 92 )A70 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 125 )A93 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 241 )A126 - 241
5X-RAY DIFFRACTION5chain 'A' and (resid 242 through 285 )A242 - 285
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 34 )B5 - 34
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 52 )B35 - 52
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 92 )B53 - 92
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 112 )B93 - 112
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 148 )B113 - 148
11X-RAY DIFFRACTION11chain 'B' and (resid 149 through 161 )B149 - 161
12X-RAY DIFFRACTION12chain 'B' and (resid 162 through 184 )B162 - 184
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 219 )B185 - 219
14X-RAY DIFFRACTION14chain 'B' and (resid 220 through 241 )B220 - 241
15X-RAY DIFFRACTION15chain 'B' and (resid 242 through 258 )B242 - 258
16X-RAY DIFFRACTION16chain 'B' and (resid 259 through 285 )B259 - 285

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