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- PDB-3qq0: Crystal structure of a deletion mutant (N59) of 3-deoxy-D-manno-o... -

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Basic information

Entry
Database: PDB / ID: 3qq0
TitleCrystal structure of a deletion mutant (N59) 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: 1.9 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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)121,99312
Polymers121,6214
Non-polymers3728
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-59 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.058, 85.744, 163.187
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
1116A4 - 59
2116B4 - 59
3116C4 - 59
4116D4 - 59
1216A71 - 203
2216B71 - 203
3216C71 - 203
4216D71 - 203
1316A218 - 237
2316B218 - 237
3316C218 - 237
4316D218 - 237
1416A258 - 275
2416B258 - 276
3416C258 - 275
4416D258 - 275

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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: 30405.229 Da / Num. of mol.: 4 / Mutation: DEL(N59)
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.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 47.88 %
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: Dec 14, 2009
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: 1.9→36.66 Å / Num. all: 91249 / Num. obs: 91249 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.52 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.9-1.974.360.3573.48783197.3
1.97-2.044.60.3093.391171100
2.04-2.144.350.2584.59021199.9
2.14-2.254.560.216590961100
2.25-2.394.50.1686.69109199.9
2.39-2.584.620.1237.691351100
2.58-2.834.570.08910.99147199.9
2.83-3.244.690.06213.59179199.9
3.24-4.094.510.04618.79229199.3
4.09-36.844.450.03823.49433198.3

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Processing

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

2qkf


Resolution: 1.9→32.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2303 / WRfactor Rwork: 0.1891 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8558 / SU B: 7.076 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1434 / SU Rfree: 0.1365 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 4579 5 %RANDOM
Rwork0.1887 ---
all0.1906 91174 --
obs0.1906 91174 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 28.93 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7410 0 18 717 8145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227688
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.97910441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93925.215303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.028151331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1561524
X-RAY DIFFRACTIONr_chiral_restr0.080.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215646
X-RAY DIFFRACTIONr_mcbond_it1.1391.54934
X-RAY DIFFRACTIONr_mcangle_it1.96627969
X-RAY DIFFRACTIONr_scbond_it3.08332754
X-RAY DIFFRACTIONr_scangle_it4.9714.52454
Refine LS restraints NCS

Ens-ID: 1 / Number: 1564 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.595
2BLOOSE POSITIONAL0.495
3CLOOSE POSITIONAL0.455
4DLOOSE POSITIONAL0.465
1ALOOSE THERMAL3.2310
2BLOOSE THERMAL2.9410
3CLOOSE THERMAL3.2610
4DLOOSE THERMAL3.0510
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 340 -
Rwork0.28 6056 -
all-6396 -
obs--95.25 %
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)
10.7792-0.0604-0.51470.5996-0.09610.9546-0.01140.1934-0.0253-0.11290.01320.0034-0.0332-0.2302-0.00180.1307-0.0033-0.00270.1878-0.00590.00768.68921.26548.074
20.5098-0.2790.13040.4101-0.00270.6109-0.0272-0.03010.0126-0.00140.0021-0.00440.0207-0.01640.02510.1118-0.01570.0130.1283-0.0050.014916.05213.34484.082
30.1084-0.18570.03830.486-0.18470.877-0.008-0.0339-0.0096-0.0486-0.0152-0.00620.0398-0.04420.02320.1307-0.01450.01370.1108-0.01090.016333.36-1.38337.556
40.2722-0.3635-0.09551.33320.9021.5776-0.0634-0.00150.05610.28010.00350.0090.34920.05710.05990.20460.01840.00750.0891-0.00080.019939.529-10.89173.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 276
3X-RAY DIFFRACTION3C1 - 275
4X-RAY DIFFRACTION4D1 - 275

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