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- PDB-4jte: Crystal structure of F114A mutant of 3-deoxy-D-manno-octulosonate... -

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Basic information

Entry
Database: PDB / ID: 4jte
TitleCrystal structure of F114A 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 / BIOSYNTHESIS / 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. / 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)121,8677
Polymers121,7734
Non-polymers943
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-78 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.355, 85.473, 163.057
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: 30443.232 Da / Num. of mol.: 4 / Mutation: F114A
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
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 5, 2007
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→39.95 Å / Num. obs: 88194 / % possible obs: 97.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Χ2: 0.97 / Net I/σ(I): 8.8 / Scaling rejects: 3133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.9-1.974.370.6011.23382877311.1487
1.97-2.054.730.4882.34217789111.06100
2.05-2.144.760.4232.64271489661.09100
2.14-2.254.650.3822.43927583851.1794
2.25-2.394.720.2913.44261389371.1499.8
2.39-2.584.770.1785.34286789600.98100
2.58-2.844.740.1197.74301890140.9100
2.84-3.254.730.07311.94312190390.8299.9
3.25-4.094.740.051174262088420.7796.8
4.09-39.954.730.0330.64535494090.6999.8

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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: 1.9→39.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2555 / WRfactor Rwork: 0.2175 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7627 / SU B: 9.734 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1791 / SU Rfree: 0.1632 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 4369 5 %RANDOM
Rwork0.2286 ---
obs0.2305 87105 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.96 Å2 / Biso mean: 46.8224 Å2 / Biso min: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å2-0 Å2
2--0.6 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 0 3 324 8059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197888
X-RAY DIFFRACTIONr_bond_other_d0.0090.027837
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.97510671
X-RAY DIFFRACTIONr_angle_other_deg1.583318005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58851011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22224.825315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.393151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6371533
X-RAY DIFFRACTIONr_chiral_restr0.0930.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218859
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021710
X-RAY DIFFRACTIONr_mcbond_it2.7272.9684071
X-RAY DIFFRACTIONr_mcbond_other2.7272.9674070
X-RAY DIFFRACTIONr_mcangle_it3.7724.4265073
LS refinement shellResolution: 1.9→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 293 -
Rwork0.5 5125 -
all-5418 -
obs--82.95 %
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)
12.0189-0.5856-0.75690.8834-0.2472.0604-0.02640.3966-0.0947-0.18870.00370.14630.1184-0.34940.02270.0878-0.0165-0.03240.16890.00120.09017.871420.651747.8706
21.0255-0.57520.44811.4791-0.17132.2734-0.0445-0.01740.08010.02070.014-0.0663-0.0648-0.02590.03050.0143-0.01340.01750.066-0.01390.04915.690113.944283.6759
30.9318-0.53170.12810.789-0.48332.2232-0.0354-0.04180.0726-0.0329-0.0134-0.0287-0.13220.02460.04880.0729-0.01790.0020.0593-0.02610.05533.3704-1.45437.9573
41.553-1.662-0.47473.13841.0162.8589-0.3049-0.2325-0.05640.68670.24980.17730.5028-0.00610.05510.23060.07740.01790.087-0.01010.070836.9952-11.840473.4289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B1 - 277
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D1 - 276

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