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- PDB-5d02: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5d02
TitleNeisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / Allostery / DAH7PS
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
: / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsHeyes, L.C.
CitationJournal: To Be Published
Title: Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant at 1.87 Angstroms resolution
Authors: Heyes, L.C.
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 / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)156,23919
Polymers154,8454
Non-polymers1,39415
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-102 kcal/mol
Surface area43980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.540, 135.546, 76.009
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: 38711.152 Da / Num. of mol.: 4 / Mutation: E176Q
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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 5 types, 655 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.48 Å3/Da / Density % sol: 50.38 % / 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: 1.87→75.55 Å / Num. obs: 121730 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.87→75.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.788 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22075 7573 6.2 %RANDOM
Rwork0.17615 ---
obs0.17891 114105 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.721 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20.41 Å2
2--1.41 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.87→75.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10117 0 74 640 10831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910452
X-RAY DIFFRACTIONr_bond_other_d0.0010.029934
X-RAY DIFFRACTIONr_angle_refined_deg1.451.96114177
X-RAY DIFFRACTIONr_angle_other_deg0.816322767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37651347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03923.833454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.642151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.011573
X-RAY DIFFRACTIONr_chiral_restr0.0860.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022371
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_it1.3062.2825379
X-RAY DIFFRACTIONr_mcbond_other1.3052.2825378
X-RAY DIFFRACTIONr_mcangle_it1.9093.4136729
X-RAY DIFFRACTIONr_mcangle_other1.9093.4136730
X-RAY DIFFRACTIONr_scbond_it1.8552.5355073
X-RAY DIFFRACTIONr_scbond_other1.8412.5275066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7563.7057437
X-RAY DIFFRACTIONr_long_range_B_refined5.45319.33712137
X-RAY DIFFRACTIONr_long_range_B_other5.45219.34112138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 559 -
Rwork0.288 8429 -
obs--99.93 %
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)
12.11820.214-0.08730.8957-0.42170.6998-0.06770.0983-0.262-0.2053-0.0393-0.12120.17520.03930.1070.1221-0.00690.0230.025-0.01910.0813-3.447-86.6577-7.5684
21.4762-0.1058-0.17520.7965-0.59661.366-0.0354-0.03250.0942-0.02040.23350.14390.0652-0.3238-0.19810.0327-0.0321-0.04770.12760.07410.0899-35.1054-73.75450.2588
31.95710.8177-0.21462.2337-0.97131.07980.04430.07230.0694-0.061-0.0502-0.1786-0.01740.01420.00590.043-0.00190.01790.0560.04710.06025.0311-37.1087-30.3298
42.06780.18610.90640.5721-0.04930.77920.07110.35110.0977-0.1051-0.00010.15460.06780.1587-0.07090.10380.0323-0.03910.21370.10980.1326-26.9241-43.0894-44.9702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 349
2X-RAY DIFFRACTION2B15 - 349
3X-RAY DIFFRACTION3C16 - 349
4X-RAY DIFFRACTION4D16 - 349

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