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

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Basic information

Entry
Database: PDB / ID: 5dcd
TitleNeisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated (Tyrosine)
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / Allostery / aromatic amino acid / regulated / ligand
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
: / trimethylamine oxide / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsHeyes, L.C. / Parker, E.
CitationJournal: To Be Published
Title: Structure of Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP at 2.05 Angstroms
Authors: Heyes, L.C. / Parker, E.J.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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 / citation / database_2 / diffrn_source / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)156,19017
Polymers154,8494
Non-polymers1,34113
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.938, 141.292, 74.675
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 5 - 349 / Label seq-ID: 5 - 349

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11CC
21AA
12CC
22BB
13CC
23DD

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.947685, 0.25281, 0.194883), (0.238152, -0.966503, 0.095689), (0.212546, -0.044271, -0.976148)-0.69896, 30.27004, -31.18134

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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: 38712.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: aroG, NMB0307 / Details (production host): 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 , 5 types, 303 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9NO
#5: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.52 Å3/Da / Density % sol: 51.15 % / 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: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.31→74.23 Å / Num. obs: 65792 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.1
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.31→74.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.136 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 3299 5 %RANDOM
Rwork0.19382 ---
obs0.19608 62183 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.883 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0.1 Å2
2--0.12 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.31→74.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10367 0 81 290 10738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210047
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.95914486
X-RAY DIFFRACTIONr_angle_other_deg0.801323019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54951384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23923.885453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.218151698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491566
X-RAY DIFFRACTIONr_chiral_restr0.0760.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022394
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_it1.052.2925554
X-RAY DIFFRACTIONr_mcbond_other1.052.2925553
X-RAY DIFFRACTIONr_mcangle_it1.6563.4336932
X-RAY DIFFRACTIONr_mcangle_other1.6553.4336933
X-RAY DIFFRACTIONr_scbond_it1.3272.4455110
X-RAY DIFFRACTIONr_scbond_other1.3272.4455110
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0873.6157555
X-RAY DIFFRACTIONr_long_range_B_refined4.10618.71612067
X-RAY DIFFRACTIONr_long_range_B_other4.10618.71712068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
14994LOOSE POSITIONAL0.325
14994LOOSE THERMAL1.5410
24860LOOSE POSITIONAL0.265
24860LOOSE THERMAL1.8910
34983LOOSE POSITIONAL0.315
34983LOOSE THERMAL1.5210
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 263 -
Rwork0.241 4553 -
obs--99.83 %
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)
11.54270.0170.16811.46090.92411.05820.06280.09610.00160.1133-0.06690.03380.1036-0.06890.00410.17720.00740.01040.0131-0.00450.07-28.297-14.1796-28.7736
21.91030.3073-0.44781.31031.01762.5844-0.05720.0158-0.13890.07820.2507-0.23070.44030.5307-0.19350.16060.0893-0.02390.1532-0.07530.20361.131-2.829-36.8145
32.3487-0.26090.29921.8560.30091.10520.0455-0.2237-0.030.3033-0.00320.1512-0.0661-0.0621-0.04230.1321-0.00850.04760.0243-0.00670.0638-36.676634.5877-8.7711
41.7983-0.08170.60260.63730.18621.47940.0028-0.04610.18240.0488-0.0081-0.1028-0.18940.01320.00530.1796-0.0434-0.00380.0317-0.0410.143-6.847629.9674.6732
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 DIFFRACTION4D4 - 349

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