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- PDB-3qq1: Crystal structure of a double mutant [A58P, DEL(N59)] of 3-deoxy-... -

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Basic information

Entry
Database: PDB / ID: 3qq1
TitleCrystal structure of a double mutant [A58P, DEL(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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)121,7254
Polymers121,7254
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-67 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.820, 85.150, 163.780
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:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 2001 - 200
21METMETLEULEUBB1 - 2001 - 200
31METMETLEULEUCC1 - 2001 - 200
41METMETLEULEUDD1 - 2001 - 200
12ALAALALEULEUAA215 - 234215 - 234
22ALAALALEULEUBB215 - 234215 - 234
32ALAALALEULEUCC215 - 234215 - 234
42ALAALALEULEUDD215 - 234215 - 234
13HISHISILEILEAA254 - 275254 - 275
23HISHISILEILEBB254 - 275254 - 275
33HISHISILEILECC254 - 275254 - 275
43HISHISILEILEDD254 - 275254 - 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: 30431.264 Da / Num. of mol.: 4 / Mutation: A58P, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0.63 °
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: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→54.593 Å / Num. all: 32102 / Num. obs: 32102 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.119 / Net I/σ(I): 10.2
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
2.7-2.854.80.5640.5031.52233246200.2510.5640.5033.299.5
2.85-3.024.90.4010.3582.12117843550.1780.4010.3584.499.7
3.02-3.234.80.2710.2413.21955940880.1220.2710.2416.199.4
3.23-3.494.80.1740.1544.91843838730.0780.1740.1548.799.8
3.49-3.824.70.1180.10471657235370.0540.1180.10411.899.9
3.82-4.274.70.0960.0858.21508832400.0440.0960.08514.399.9
4.27-4.934.40.0910.0881266628780.0430.0910.0816.999.9
4.93-6.044.30.0820.0728.51030624240.0390.0820.07215.999.1
6.04-8.544.80.0510.04512.8932019450.0230.0510.04517.9100
8.54-54.5934.50.0330.02919.5511711420.0150.0330.02922.399.4

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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 2QKF

2qkf


Resolution: 2.7→47.89 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.859 / WRfactor Rfree: 0.2652 / WRfactor Rwork: 0.2018 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8208 / SU B: 28.664 / SU ML: 0.273 / SU R Cruickshank DPI: 0.2872 / SU Rfree: 0.3843 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1562 4.9 %RANDOM
Rwork0.2112 ---
all0.2143 32051 --
obs0.2143 32051 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.57 Å2 / Biso mean: 34.3241 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2--0.41 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7662 0 0 139 7801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227880
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.97910669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08251004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30525.016321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.072151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4071530
X-RAY DIFFRACTIONr_chiral_restr0.0760.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215774
X-RAY DIFFRACTIONr_mcbond_it0.6551.54990
X-RAY DIFFRACTIONr_mcangle_it1.25128072
X-RAY DIFFRACTIONr_scbond_it1.42432890
X-RAY DIFFRACTIONr_scangle_it2.6454.52591
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A957MEDIUM POSITIONAL0.380.5
2B957MEDIUM POSITIONAL0.410.5
3C957MEDIUM POSITIONAL0.320.5
4D957MEDIUM POSITIONAL0.320.5
1A861LOOSE POSITIONAL0.75
2B861LOOSE POSITIONAL0.795
3C861LOOSE POSITIONAL0.685
4D861LOOSE POSITIONAL0.715
1A957MEDIUM THERMAL0.322
2B957MEDIUM THERMAL0.362
3C957MEDIUM THERMAL0.292
4D957MEDIUM THERMAL0.332
1A861LOOSE THERMAL0.4210
2B861LOOSE THERMAL0.4210
3C861LOOSE THERMAL0.3810
4D861LOOSE THERMAL0.4110
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 101 -
Rwork0.257 2238 -
all-2339 -
obs--99.41 %
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)
11.45490.0455-0.32040.5203-0.17390.9624-0.09560.2807-0.05060.02010.0048-0.05020.0128-0.17070.09080.0855-0.01930.02250.2054-0.01390.02288.08820.52348.055
20.9143-0.2110.6550.6141-0.2930.7267-0.0373-0.07810.0233-0.0331-0.0094-0.03520.0361-0.10240.04680.0981-0.00050.01960.1664-0.02850.014415.78113.79584.143
30.3819-0.45120.30520.5256-0.391.4263-0.0475-0.01880.0136-0.0148-0.0263-0.02890.0036-0.07370.07380.166-0.01250.02810.1413-0.02570.013833.557-1.40937.989
40.0957-0.2694-0.1681.35590.39681.5203-0.02260.07410.0330.28980.01670.1010.3260.06280.00590.25350.01950.03540.10380.0110.048137.885-11.42673.916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B1 - 278
3X-RAY DIFFRACTION3C1 - 276
4X-RAY DIFFRACTION4D1 - 276

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