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- PDB-4jtl: Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate... -

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Basic information

Entry
Database: PDB / ID: 4jtl
TitleCrystal structure of F139G 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 / 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: 2.1 Å
AuthorsAllison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2013
Title: Examining the Role of Intersubunit Contacts in Catalysis by 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase.
Authors: Allison, T.M. / Cochrane, F.C. / Jameson, G.B. / Parker, E.J.
History
DepositionMar 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Sep 20, 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)121,7886
Polymers121,7174
Non-polymers712
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-74 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.997, 85.924, 163.370
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: 30429.205 Da / Num. of mol.: 4 / Mutation: F139G
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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
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, cryoprotectant solution, comprising 20% glycerol and reservoir ...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, cryoprotectant solution, comprising 20% glycerol and reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP

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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: Feb 5, 2010
RadiationMonochromator: AXCO PX70 CAPILLARY OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→38.06 Å / Num. obs: 62633 / % possible obs: 92 % / Redundancy: 3.12 % / Rmerge(I) obs: 0.08 / Χ2: 0.94 / Net I/σ(I): 7.2 / Scaling rejects: 6715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.183.080.3952.32143766921.1599.9
2.18-2.262.960.3732.41703155431.0982.3
2.26-2.373.110.3022.82144966981.0499.8
2.37-2.493.150.2373.31895859090.9187.8
2.49-2.653.140.1824.52031363310.9893.3
2.65-2.853.160.1425.72203567590.9599.9
2.85-3.143.230.1037.42229067740.8499.9
3.14-3.593.120.07110.52183666900.8697.7
3.59-4.523.010.05114.91430544680.8365
4.52-38.063.160.04318.92235567690.7594.6

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
d*TREK9.4SSIdata reduction
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QKF

2qkf


Resolution: 2.1→37.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.2124 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8057 / SU B: 11.955 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2548 / SU Rfree: 0.2005 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 3143 5 %RANDOM
Rwork0.217 ---
obs0.2186 62592 91.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.54 Å2 / Biso mean: 40.4761 Å2 / Biso min: 18.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20 Å2
2--1.42 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 2 130 7891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197927
X-RAY DIFFRACTIONr_bond_other_d0.0090.027899
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.97710715
X-RAY DIFFRACTIONr_angle_other_deg1.507318176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91951008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87525.061326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.753151421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0161532
X-RAY DIFFRACTIONr_chiral_restr0.0950.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218879
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021711
X-RAY DIFFRACTIONr_mcbond_it2.8073.0514054
X-RAY DIFFRACTIONr_mcbond_other2.8073.054053
X-RAY DIFFRACTIONr_mcangle_it4.0414.5545050
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 259 -
Rwork0.305 4588 -
all-4847 -
obs--97.17 %
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)
11.0044-0.0874-0.29270.43430.20130.7506-0.03910.17620.0103-0.0345-0.00920.0319-0.0713-0.16390.04830.04620.0216-0.00740.10040.010.01078.0620.99847.925
20.5063-0.33950.1110.74610.13650.486-0.0436-0.01930.05140.01530.03930.00630.0270.01020.00430.0478-0.01030.01740.0547-0.00890.026615.5713.7884.005
30.2463-0.1247-0.09880.25540.00220.7105-0.0187-0.0465-0.0036-0.0549-0.0074-0.0063-0.0198-0.04540.0260.0886-0.0065-0.00030.0475-0.01190.010333.614-1.37637.836
40.3735-0.6911-0.42371.70030.41091.0604-0.1282-0.0182-0.02150.28060.07960.0530.26350.07880.04860.16830.05270.0130.04440.00650.021237.918-11.54373.614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 277
2X-RAY DIFFRACTION2B1 - 279
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D1 - 277

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