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- PDB-2qkf: Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate syn... -

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Basic information

Entry
Database: PDB / ID: 2qkf
TitleCrystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Components3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
KeywordsTRANSFERASE / MANNO-OCTULOSONATE / SYNTHASE / LIPOPOLYSACCHARIDE / KDOP / KDO8 KDOPS / KDO8PS / TIM barrel / Lipopolysaccharide biosynthesis / LYASE
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 serogroup B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCochrane, F.C. / Patchett, M.L. / Jameson, G.B. / Parker, E.J.
Citation
Journal: To be Published
Title: Re-Establishing a Metal-Binding Scaffold with Full Activity in the Metal-Independent Kdo8P Synthase from Neisseria Meningitidis
Authors: Cochrane, F.C. / Patchett, M.L. / Jameson, G.B. / Parker, E.J.
#1: Journal: Org.Biomol.Chem. / Year: 2005
Title: Mechanistic Divergence of Two Closely Related Aldol-Like Enzyme-Catalysed Reactions
Authors: Ahn, M. / Pietersma, A.L. / Schofield, L.R. / Parker, E.J.
#2: Journal: To be Published
Title: Arabinose 5-Phosphate Analogues as Mechanistic Probes for Neisseria meningitidis 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase
Authors: Ahn, M. / Cochrane, F.C. / Patchett, M.L. / Parker, E.J.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / 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.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
B: 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
C: 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
D: 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,64614
Polymers122,0774
Non-polymers56910
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-130.7 kcal/mol
Surface area34170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.515, 85.295, 162.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS5AA2 - 522 - 52
21ASPASPLYSLYS5BB2 - 522 - 52
31ASPASPLYSLYS5CC2 - 522 - 52
41ASPASPLYSLYS5DD2 - 522 - 52
52ALAALAVALVAL6AA53 - 6953 - 69
62ALAALAVALVAL6BB53 - 6953 - 69
72ALAALAVALVAL6CC53 - 6953 - 69
82ALAALAVALVAL6DD53 - 6953 - 69
93GLYGLYALAALA5AA70 - 11370 - 113
103GLYGLYALAALA5BB70 - 11370 - 113
113GLYGLYALAALA5CC70 - 11370 - 113
123GLYGLYALAALA5DD70 - 11370 - 113
134ASPASPGLUGLU5AA220 - 236220 - 236
144ASPASPGLUGLU5BB220 - 236220 - 236
154ASPASPGLUGLU5CC220 - 236220 - 236
164ASPASPGLUGLU5DD220 - 236220 - 236
175LEULEUGLNGLN5AA256 - 274256 - 274
185LEULEUGLNGLN5BB256 - 274256 - 274
195LEULEUGLNGLN5CC256 - 274256 - 274
205LEULEUGLNGLN5DD256 - 274256 - 274
216PHEPHELEULEU6AA114 - 121114 - 121
226PHEPHELEULEU6BB114 - 121114 - 121
236PHEPHELEULEU6CC114 - 121114 - 121
246PHEPHELEULEU6DD114 - 121114 - 121
257VALVALVALVAL5AA122 - 197122 - 197
267VALVALVALVAL5BB122 - 197122 - 197
277VALVALVALVAL5CC122 - 197122 - 197
287VALVALVALVAL5DD122 - 197122 - 197
298VALVALSERSER6AA197 - 200197 - 200
308VALVALSERSER6BB197 - 200197 - 200
318VALVALSERSER6CC197 - 200197 - 200
328VALVALSERSER6DD197 - 200197 - 200

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Components

#1: Protein
3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase / 2-dehydro-3-deoxyphosphooctonate aldolase / Phospho-2- dehydro-3-deoxyoctonate aldolase / KDO-8- ...2-dehydro-3-deoxyphosphooctonate aldolase / Phospho-2- dehydro-3-deoxyoctonate aldolase / KDO-8-phosphate synthetase / KDO 8-P synthase / KDOPS


Mass: 30519.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: kdsA / 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.32 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / pH: 4.6
Details: CRYSTALLISATION CONDITIONS: 18.6 MG/ML PROTEIN MIXED 1:1 WITH RESERVOIR LIQUOR CONTAINING 100 MM SODIUM ACETATE PH 4.60, 200 MICROMOLAR PEP, 0.6, 1.6 MOLAR SODIUM CHLORIDE, VAPOR DIFFUSION, ...Details: CRYSTALLISATION CONDITIONS: 18.6 MG/ML PROTEIN MIXED 1:1 WITH RESERVOIR LIQUOR CONTAINING 100 MM SODIUM ACETATE PH 4.60, 200 MICROMOLAR PEP, 0.6, 1.6 MOLAR SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2005 / Details: OSMIC BLUE MIRRORS
RadiationMonochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.95 % / Av σ(I) over netI: 13.4 / Number: 463387 / Rmerge(I) obs: 0.043 / Χ2: 0.89 / D res high: 1.75 Å / D res low: 39.9 Å / Num. obs: 111333 / % possible obs: 97
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.7739.999.90.0230.774.162098
2.993.7799.90.0370.734.281611
2.612.9999.80.0570.774.212296
2.382.6199.70.0790.834.152513
2.22.3899.60.1070.884.12668
2.072.299.10.150.934.052897
1.972.0799.10.2110.994.042690
1.891.9798.80.2751.0542946
1.811.8995.20.331.083.522247
1.751.8178.20.3681.122.711204
ReflectionResolution: 1.75→40 Å / Num. obs: 111333 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.95 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / % possible all: 78.2

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D9E

1d9e


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.815 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS STATE THAT THE SIDECHAINS OF HIS D 94, ARG B 165 and ASN B 190 HAVE TWO DISTINCT CONFORMATIONS, WITH AN HOH IN SITE A WHEN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS STATE THAT THE SIDECHAINS OF HIS D 94, ARG B 165 and ASN B 190 HAVE TWO DISTINCT CONFORMATIONS, WITH AN HOH IN SITE A WHEN THE SIDECHAIN IS IN SITE B. HOH A 313 AND HOH A 380 ARE PRESENT IN HALF OCCUPANCY. THE AUTHORS DO NOT BELIEVE THAT THE CLOSE CONTACTS BETWEEN LYS 76C AND GLU 40D REPRESENT AN INTERMOLECULAR ISOPEPTIDE BOND. THE AUTHORS STATE THAT RESIDUES ASN 6 AND ARG 229 SHARE COMMON, WELL-DEFINED PEPTIDE CONFORMATIONS IN ALL SUBUNITS. OTHER RESIDUES ARE AT THE STARTS AND ENDS OF LOOPS THAT HAVE POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5588 5 %RANDOM
Rwork0.196 ---
obs0.197 105744 97 %-
all-111333 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.2 Å20 Å2
3----1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.119 Å0.121 Å
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 30 528 8306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228100
X-RAY DIFFRACTIONr_bond_other_d0.0010.027650
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.97610990
X-RAY DIFFRACTIONr_angle_other_deg0.817317838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61951058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99425330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.796151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8251530
X-RAY DIFFRACTIONr_chiral_restr0.0730.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021529
X-RAY DIFFRACTIONr_nbd_refined0.2130.21651
X-RAY DIFFRACTIONr_nbd_other0.2220.27053
X-RAY DIFFRACTIONr_nbtor_refined0.170.23841
X-RAY DIFFRACTIONr_nbtor_other0.1120.23620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.86935121
X-RAY DIFFRACTIONr_mcbond_other0.66532098
X-RAY DIFFRACTIONr_mcangle_it2.87458300
X-RAY DIFFRACTIONr_scbond_it1.04122979
X-RAY DIFFRACTIONr_scangle_it1.68332667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1166medium positional0.190.5
2B1166medium positional0.390.5
3C1166medium positional0.190.5
4D1166medium positional0.250.5
1A2066loose positional0.715
2B2066loose positional0.885
3C2066loose positional0.655
4D2066loose positional0.845
1A1166medium thermal3.74
2B1166medium thermal2.984
3C1166medium thermal3.114
4D1166medium thermal2.384
1A2066loose thermal5.2310
2B2066loose thermal4.7210
3C2066loose thermal3.7710
4D2066loose thermal3.2210
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 321 -
Rwork0.323 6041 -
obs--76.05 %

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