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- PDB-3qpy: Crystal structure of a mutant (K57A) of 3-deoxy-D-manno-octuloson... -

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Basic information

Entry
Database: PDB / ID: 3qpy
TitleCrystal structure of a mutant (K57A) 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAllison, T.M. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2011
Title: Targeting the role of a key conserved motif for substrate selection and catalysis by 3-deoxy-D-manno-octulosonate 8-phosphate synthase
Authors: Allison, T.M. / Hutton, R.D. / Cochrane, F.C. / Yeoman, J.A. / Jameson, G.B. / Parker, E.J.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0669
Polymers121,8454
Non-polymers2215
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-60 kcal/mol
Surface area36100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.428, 86.183, 163.312
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
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A4 - 203
2115B4 - 203
3115C4 - 203
4115D4 - 203
1215A219 - 239
2215B219 - 239
3215C219 - 239
4215D219 - 239
1315A259 - 279
2315B259 - 279
3315C259 - 279
4315D259 - 279

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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: 30461.225 Da / Num. of mol.: 4 / Mutation: K57A
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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.38 Å3/Da / Density % sol: 48.33 % / Mosaicity: 0.365 °
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: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2010
RadiationMonochromator: AXCO PX70 CAPILLARY OPTIC / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→34.59 Å / Num. all: 83787 / Num. obs: 83787 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.15 % / Rmerge(I) obs: 0.079 / Χ2: 0.91 / Net I/σ(I): 8.6 / Scaling rejects: 21111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.95-2.025.160.39434518284321.091665100
2.02-2.15.170.3313.44540484531.051691100
2.1-2.25.20.2763.945562842511743100
2.2-2.314.760.2623.43766674821.06205388.4
2.31-2.465.250.16964636184850.921850100
2.46-2.655.270.1337.54671285150.86183399.9
2.65-2.915.290.1019.44699685270.811865100
2.91-3.335.320.07612.24748685640.75196199.8
3.33-4.25.170.06215.54412581080.77224493.9
4.2-34.594.870.04921.54706787960.8420698

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QKF

2qkf


Resolution: 1.95→33.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2546 / WRfactor Rwork: 0.2051 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8014 / SU B: 9.382 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1787 / SU Rfree: 0.1657 / Cross valid method: THROUGHOUT / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 4210 5 %RANDOM
Rwork0.2048 ---
all0.2071 83643 --
obs0.2071 83643 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.48 Å2 / Biso mean: 37.0264 Å2 / Biso min: 17.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--0.94 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 10 737 8435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227958
X-RAY DIFFRACTIONr_angle_refined_deg1.091.97610786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62351026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67524.833329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.718151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5731535
X-RAY DIFFRACTIONr_chiral_restr0.0920.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215855
X-RAY DIFFRACTIONr_mcbond_it1.3971.55036
X-RAY DIFFRACTIONr_mcangle_it2.41328149
X-RAY DIFFRACTIONr_scbond_it3.87432922
X-RAY DIFFRACTIONr_scangle_it6.3654.52624
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A908MEDIUM POSITIONAL0.350.5
2B908MEDIUM POSITIONAL0.390.5
3C908MEDIUM POSITIONAL0.250.5
4D908MEDIUM POSITIONAL0.260.5
1A806LOOSE POSITIONAL0.745
2B806LOOSE POSITIONAL0.835
3C806LOOSE POSITIONAL0.75
4D806LOOSE POSITIONAL0.775
1A908MEDIUM THERMAL2.092
2B908MEDIUM THERMAL3.462
3C908MEDIUM THERMAL2.482
4D908MEDIUM THERMAL3.732
1A806LOOSE THERMAL2.4810
2B806LOOSE THERMAL3.3610
3C806LOOSE THERMAL2.5210
4D806LOOSE THERMAL3.3210
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 322 -
Rwork0.317 5891 -
all-6213 -
obs--99.97 %
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)
10.4021-0.0645-0.33430.15360.0920.73150.0140.1285-0.0348-0.05-0.0292-0.0276-0.0691-0.20410.01520.35260.02660.00140.21360.01210.07387.79420.61847.819
20.4934-0.28570.0290.16560.08390.5901-0.0408-0.05980.0404-0.01930.05320.01460.0495-0.021-0.01250.3274-0.00310.01810.1506-0.00480.097415.76513.78984.043
30.1917-0.2352-0.00790.22740.00340.7065-0.003-0.04080.0022-0.066-0.0116-0.02370.0294-0.04040.01460.3831-0.00720.00820.1223-0.02010.085633.97-1.41137.826
4-0.0864-0.8722-0.47111.42980.77521.3635-0.23440.06750.12620.40780.21140.03940.4450.11070.02290.51880.0885-0.00350.0952-0.04380.067837.677-11.66973.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B1 - 278
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D1 - 276

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