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- PDB-4jth: Crystal structure of F114R/R117Q mutant of 3-deoxy-D-manno-octulo... -

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Basic information

Entry
Database: PDB / ID: 4jth
TitleCrystal structure of F114R/R117Q 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)122,29311
Polymers122,0014
Non-polymers2927
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-127 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.150, 85.990, 163.110
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: 30500.279 Da / Num. of mol.: 4 / Mutation: F114R, R117Q
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.: 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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 47.9 %
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 1.6 M NaCl. cryoprotectant 20% glycerol and the reservoir solution, Vapor ...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 1.6 M NaCl. cryoprotectant 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→45.955 Å / Num. all: 78806 / Num. obs: 78806 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.115 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.117.30.377282658113580.377100
2.11-2.247.30.2752.778245107590.275100
2.24-2.397.30.2063.673466101310.206100
2.39-2.587.20.1554.66842394590.155100
2.58-2.837.20.125.66279487310.12100
2.83-3.167.10.1016.25652779310.101100
3.16-3.6570.09764944570140.097100
3.65-4.476.80.0995.74046659890.099100
4.47-6.326.80.0826.23200347190.082100
6.32-45.9556.90.06771868627150.06799.7

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QKF

2qkf


Resolution: 2→45.955 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.1647 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8956 / SU B: 5.914 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1524 / SU Rfree: 0.1357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3931 5 %RANDOM
Rwork0.159 ---
obs0.1608 78725 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.06 Å2 / Biso mean: 28.1477 Å2 / Biso min: 10.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20 Å2
2--0.06 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2→45.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 12 795 8614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198130
X-RAY DIFFRACTIONr_bond_other_d0.010.028087
X-RAY DIFFRACTIONr_angle_refined_deg1.821.97611032
X-RAY DIFFRACTIONr_angle_other_deg1.682318638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7551058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67625.104335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.986151459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.811532
X-RAY DIFFRACTIONr_chiral_restr0.1110.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219189
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021763
X-RAY DIFFRACTIONr_mcbond_it2.1811.7994145
X-RAY DIFFRACTIONr_mcbond_other2.181.7984144
X-RAY DIFFRACTIONr_mcangle_it3.2762.6665190
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 287 -
Rwork0.192 5465 -
all-5752 -
obs--100 %
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)
10.6927-0.0763-0.44430.42440.20650.6814-0.01750.14950.0189-0.09070.00020.072-0.0816-0.15770.01730.04180.013-0.02370.09730.02310.02848.26621.01748.158
20.3961-0.30490.05760.76150.01690.6188-0.0462-0.04630.06480.03520.05030.02030.0609-0.0236-0.00410.02540.00110.00940.0642-0.00570.049915.77413.68983.728
30.2196-0.1355-0.08230.3529-0.07060.7069-0.0143-0.04360.0103-0.06860.0039-0.0210.0166-0.02860.01040.072-0.00410.00990.0388-0.01150.015633.611-1.13237.873
40.3694-0.5394-0.40681.34330.51251.0852-0.1318-0.0260.01810.2570.1069-0.01040.28620.08560.02480.13180.0532-0.0120.0298-0.00790.021537.934-11.50673.334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 277
2X-RAY DIFFRACTION2B1 - 278
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D1 - 277

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