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- PDB-5d05: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5d05
TitleNeisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Lys107Ala variant regulated
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAH7PS / Allostery
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / 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
: / DI(HYDROXYETHYL)ETHER / PHOSPHOENOLPYRUVATE / TRIETHYLENE GLYCOL / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: To Be Published
Title: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Lys107Ala variant regulated at 1.75 Angstroms resolution
Authors: Heyes, L.C. / Parker, E.J.
History
DepositionAug 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
C: Phospho-2-dehydro-3-deoxyheptonate aldolase
D: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,12827
Polymers154,6164
Non-polymers2,51223
Water20,3931132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-166 kcal/mol
Surface area44820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.331, 141.027, 76.028
Angle α, β, γ (deg.)90.00, 97.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 38654.035 Da / Num. of mol.: 4 / Mutation: K107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: aroG, NMB0307 / Plasmid: pT7-7 / Cell line (production host): BL21* / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 8 types, 1155 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 % / Description: Monoclinic, P1211
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M Tris HCl (pH 7.3), 0.2 M trimethyl-amino-N-oxide (TMAO), 0.4 mM MnSO4 and PEG 2000MME
PH range: 7.3

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.75→74.46 Å / Num. obs: 158105 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.75→74.46 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.901 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17564 9914 6.3 %RANDOM
Rwork0.14953 ---
obs0.15118 148147 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 mean: 24.327 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.58 Å2
2---0.23 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.75→74.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10598 0 146 1132 11876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210535
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.96614913
X-RAY DIFFRACTIONr_angle_other_deg0.813324198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51751395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56123.717487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.268151859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3191581
X-RAY DIFFRACTIONr_chiral_restr0.0830.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8881.5615583
X-RAY DIFFRACTIONr_mcbond_other0.8881.5615582
X-RAY DIFFRACTIONr_mcangle_it1.3452.3356977
X-RAY DIFFRACTIONr_mcangle_other1.3442.3356978
X-RAY DIFFRACTIONr_scbond_it1.5451.8025431
X-RAY DIFFRACTIONr_scbond_other1.5451.8025431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.42.6247937
X-RAY DIFFRACTIONr_long_range_B_refined5.09814.00913462
X-RAY DIFFRACTIONr_long_range_B_other5.09814.00913463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 748 -
Rwork0.238 10921 -
obs--99.81 %
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)
10.3793-0.06890.07160.43960.13370.64530.00040.1255-0.0768-0.0234-0.02070.0446-0.03850.05460.02030.01060.01030.00430.0616-0.01610.0558-4.9772-11.3853-41.0926
20.4785-0.11120.10890.2685-0.01380.5253-0.0529-0.0507-0.04550.09230.02870.0257-0.02460.02090.02420.05130.01950.0210.01640.01450.01565.5267-10.2916-9.6876
30.3335-0.1968-0.08781.3083-0.51590.6405-0.02010.01890.0124-0.06240.02040.00750.0561-0.0306-0.00030.0107-0.00910.0010.0133-0.00640.027-23.845437.6144-30.7926
40.4428-0.0675-0.06680.8577-0.27560.5636-0.0658-0.0871-0.03780.33260.11180.1646-0.0282-0.0614-0.0460.15730.05210.08230.03690.03490.0513-34.258824.9736-2.2028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 349
2X-RAY DIFFRACTION2B4 - 349
3X-RAY DIFFRACTION3C4 - 349
4X-RAY DIFFRACTION4D3 - 349

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