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- PDB-5d03: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5d03
TitleNeisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala variant
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 / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 Å
AuthorsHeyes, L.C. / Parker, E.J.
CitationJournal: To Be Published
Title: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala variant at 1.84 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 1.1Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: diffrn_source / pdbx_struct_assembly_auth_evidence ...diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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.value / _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)156,09620
Polymers154,7364
Non-polymers1,36016
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-129 kcal/mol
Surface area43270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.256, 135.622, 75.989
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTetramer by Analytical Gel filtration

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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: 38684.082 Da / Num. of mol.: 4 / Mutation: V223A
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 , 7 types, 749 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-PEP / PHOSPHOENOLPYRUVATE


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.47 Å3/Da / Density % sol: 50.2 % / 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: 1.84→75.53 Å / Num. obs: 126857 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.4
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.84→75.53 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.197 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 7865 6.2 %RANDOM
Rwork0.16227 ---
obs0.16442 118952 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.29 Å2
2--0.42 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.84→75.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10086 0 68 733 10887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910375
X-RAY DIFFRACTIONr_bond_other_d0.0010.029869
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.96314066
X-RAY DIFFRACTIONr_angle_other_deg0.818322637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31651337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79223.822450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.391151713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.911573
X-RAY DIFFRACTIONr_chiral_restr0.0910.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022337
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_it1.2992.0635348
X-RAY DIFFRACTIONr_mcbond_other1.2972.0635347
X-RAY DIFFRACTIONr_mcangle_it1.8343.0866685
X-RAY DIFFRACTIONr_mcangle_other1.8343.0866686
X-RAY DIFFRACTIONr_scbond_it2.0772.3325027
X-RAY DIFFRACTIONr_scbond_other2.0772.3325027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.143.4017382
X-RAY DIFFRACTIONr_long_range_B_refined5.29817.70212223
X-RAY DIFFRACTIONr_long_range_B_other5.29817.70612224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 564 -
Rwork0.283 8825 -
obs--99.19 %
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)
11.5981-0.0504-0.04580.7362-0.32850.5392-0.03670.0907-0.1955-0.1444-0.0362-0.08210.14350.01980.07290.0536-0.0120.03630.0444-0.02530.0462-3.4101-86.6278-7.6109
21.1194-0.0546-0.22030.499-0.38411.0782-0.0399-0.02190.0737-0.01160.14720.08880.0821-0.2526-0.10730.0085-0.0242-0.00970.14250.03660.056-35.0191-73.58340.4515
31.28080.5907-0.02991.9871-0.65360.67930.03780.05020.0621-0.0652-0.0458-0.1597-0.02950.02790.0080.0189-0.00150.02360.0930.04910.05944.8438-37.065-30.3439
41.36230.04780.58170.6099-0.25030.64960.09510.17590.0701-0.1361-0.01260.16190.08450.0663-0.08240.04470.0283-0.02420.16090.08020.0911-26.7985-43.1168-45.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 349
2X-RAY DIFFRACTION2B17 - 349
3X-RAY DIFFRACTION3C17 - 349
4X-RAY DIFFRACTION4D17 - 349

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