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- PDB-3stg: Crystal structure of A58P, DEL(N59), and loop 7 truncated mutant ... -

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Basic information

Entry
Database: PDB / ID: 3stg
TitleCrystal structure of A58P, DEL(N59), and loop 7 truncated mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM BARREL / BIOSYNTHESIS / LYASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS
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 / cytosol
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 speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAllison, T.M. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2011
Title: An Extended (beta)7(alpha)7 Substrate-Binding Loop Is Essential for Efficient Catalysis by 3-Deoxy-D-manno-Octulosonate 8-Phosphate Synthase
Authors: Allison, T.M. / Hutton, R.D. / Jiao, W. / Gloyne, B.J. / Nimmo, E.B. / Jameson, G.B. / Parker, E.J.
History
DepositionJul 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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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)118,13816
Polymers117,7134
Non-polymers42512
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint-219 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.690, 104.050, 149.620
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: 29428.262 Da / Num. of mol.: 4 / Mutation: A58P, DEL(N59, Q202-G212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: kdsA, NMB1283 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JZ55, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.7 Å3/Da / Density % sol: 54.46 % / Mosaicity: 0.32 °
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl. Immediately prior to data collection, crystals were harvested and ...Details: 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl. Immediately prior to data collection, crystals were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95368 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 2.2→36.849 Å / Num. all: 65469 / Num. obs: 65469 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.087 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.327.40.3730.3471.86968494230.1370.3730.3476.9100
2.32-2.467.40.2710.25236642889340.0990.2710.2527.8100
2.46-2.637.40.2030.18946268284360.0740.2030.18910.1100
2.63-2.847.40.1530.1425.35816978400.0560.1530.14213100
2.84-3.117.40.1050.0987.65364372450.0390.1050.09817.6100
3.11-3.487.40.0710.06610.54861365930.0260.0710.06625100
3.48-4.027.30.0580.053124280558460.0210.0580.05333.4100
4.02-4.927.20.0440.04114.73603749770.0160.0440.04139.6100
4.92-6.967.10.0480.04512.52771839230.0180.0480.04534.9100
6.96-36.8496.40.0450.04112.21444622520.0180.0450.0414199.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3STC

3stc


Resolution: 2.2→35.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2236 / WRfactor Rwork: 0.1902 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8362 / SU B: 10.269 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2639 / SU Rfree: 0.2047 / Cross valid method: THROUGHOUT / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 3250 5 %RANDOM
Rwork0.1972 ---
all0.1992 65395 --
obs0.1992 65395 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.84 Å2 / Biso mean: 24.8155 Å2 / Biso min: 3.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 12 574 8640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228299
X-RAY DIFFRACTIONr_bond_other_d0.0010.025606
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.95711197
X-RAY DIFFRACTIONr_angle_other_deg0.867313818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64851061
X-RAY DIFFRACTIONr_chiral_restr0.0670.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021566
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 200 -
Rwork0.335 4241 -
all-4441 -
obs--100 %
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)
10.40420.29180.44630.9854-0.0420.71270.0487-0.0269-0.0487-0.09340.04410.0310.05720.0023-0.09280.1395-0.0042-0.01710.1716-0.01040.0345-23.755-36.479.053
20.1610.3184-0.39370.9015-0.49311.45720.09770.02720.01640.09070.0334-0.0039-0.2769-0.0415-0.13110.22860.04860.04660.1280.02040.0417-19.048-0.62415.078
30.1671-0.190.34010.8273-0.10190.92030.05760.0379-0.01150.08440.0045-0.02530.07650.0219-0.06210.17740.02850.00930.14730.03210.0367-19.683-42.67743.856
40.11070.0844-0.27940.79350.1810.96630.02970.03890.00190.0904-0.0122-0.0390.0015-0.0421-0.01750.13210.02180.00620.1889-0.00820.0163-19.681-6.70750.006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 268
2X-RAY DIFFRACTION2B1 - 268
3X-RAY DIFFRACTION3C1 - 268
4X-RAY DIFFRACTION4D1 - 268

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