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- PDB-4hsn: Crystal structure of DAH7PS from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 4hsn
TitleCrystal structure of DAH7PS from Neisseria meningitidis
Components3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
KeywordsTRANSFERASE / DAHP / DAHPS / DAH7PS / TIM BARREL / ALLOSTERIC REGULATION / AROMATIC BIOSYNTHESIS / SHIKIMATE PATHWAY
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCross, P.J. / Pietersma, A.L. / Allison, T.M. / Wilson-Coutts, S.M. / Cochrane, F.C. / Parker, E.J.
CitationJournal: Protein Sci. / Year: 2013
Title: Neisseria meningitidis expresses a single 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine.
Authors: Cross, P.J. / Pietersma, A.L. / Allison, T.M. / Wilson-Coutts, S.M. / Cochrane, F.C. / Parker, E.J.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
C: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
D: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,12516
Polymers154,8494
Non-polymers1,27612
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-136 kcal/mol
Surface area45410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.462, 137.279, 76.360
Angle α, β, γ (deg.)90.000, 96.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 10 - 350 / Label seq-ID: 10 - 350

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / Phospho-2-dehydro-3-deoxyheptonate aldolase / 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 (bacteria) / Strain: MC58 (serogroup B) / Gene: aroG, NMB0307 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase
#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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 ...Details: A protein solution [11 mg/mL in 10 mM BTP buffer (pH 7.3)] was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 15% 20% (w/v) PEG 2000 mme, 0.4 mM MnSO4. The drop sizes were 2 uL, and the volume of the reservoir solution was 500 uL, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→19.79 Å / Num. all: 100515 / Num. obs: 100515 / % possible obs: 99.3 %
Reflection shellResolution: 2→2.03 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XSCALEdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OF8

1of8


Resolution: 2→19.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.1796 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8641 / SU B: 7.837 / SU ML: 0.109 / SU R Cruickshank DPI: 0.169 / SU Rfree: 0.1463 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 6233 6.2 %RANDOM
Rwork0.1754 ---
obs0.1774 100477 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.47 Å2 / Biso mean: 37.0606 Å2 / Biso min: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å2-0.03 Å2
2--4.22 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10432 0 64 561 11057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910683
X-RAY DIFFRACTIONr_bond_other_d0.010.0210291
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.96814460
X-RAY DIFFRACTIONr_angle_other_deg1.478323654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52951362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39123.996463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.428151846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5361573
X-RAY DIFFRACTIONr_chiral_restr0.1130.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112124
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022365
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A210810.08
12B210810.08
21A209000.09
22C209000.09
31A213450.08
32D213450.08
41B207760.1
42C207760.1
51B209350.09
52D209350.09
61C208080.09
62D208080.09
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 494 -
Rwork0.241 6971 -
all-7465 -
obs--99.97 %
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)
12.8307-0.0382-0.3842.1699-0.43591.12070.05530.1850.33-0.0266-0.0338-0.1186-0.1056-0.0362-0.02150.2715-0.0166-0.03810.06810.05280.2311-3.445-69.646-16.549
21.2814-0.06680.10880.8777-0.08140.555-0.03480.0809-0.0483-0.0481-0.0167-0.08250.06070.01080.05150.2648-0.01-0.0040.02470.01010.22530.783-82.162-9.398
31.3204-0.254-0.0021.2108-0.77330.864-0.02410.1703-0.0825-0.05970.04120.10850.0901-0.0625-0.01710.2719-0.0295-0.02110.0326-0.03210.2174-16.548-85.374-11.432
43.84160.62811.48372.49281.06884.12870.0415-0.123-0.5691-0.001-0.08850.13870.3646-0.10570.0470.3009-0.03250.01690.0123-0.01610.3226-11.724-100.935-2.942
52.93471.90072.25938.15626.11899.8182-0.0339-0.227-0.30020.1828-0.14480.10680.37940.10510.17870.28920.00590.00390.03510.05620.34230.226-101.6142.94
61.67130.65080.19032.81590.77151.46-0.0306-0.2752-0.05540.1123-0.0972-0.0172-0.00610.06240.12780.27750.0145-0.01390.0560.04590.23184.942-85.8722.764
73.40073.03541.003110.98665.18857.4614-0.01990.0727-0.56580.0693-0.1767-0.10780.60890.04940.19660.29590.05990.06290.02280.00010.3786.306-104.375-7.281
82.18440.1272-0.11031.156-1.13942.84630.02520.17350.2691-0.01790.11090.0575-0.1601-0.0485-0.13610.23620.0025-0.01710.03230.06610.3161-31.03-62.933-8.061
92.2595-0.4478-0.50011.51380.25953.5145-0.0414-0.00470.12080.02060.21140.17270.0717-0.3556-0.170.2438-0.0331-0.0330.11990.11520.274-44.24-71.2081.071
101.74740.0825-0.30770.7051-0.74811.1563-0.05560.11950.0394-0.12340.1490.04760.1775-0.1356-0.09340.2349-0.0202-0.04030.0670.07970.2133-33.119-71.736-11.301
111.79780.1948-0.53330.8088-0.55681.0079-0.0155-0.14270.03110.03660.0129-0.01220.05670.01050.00270.2562-0.0059-0.03560.0559-0.00110.2159-22.192-73.9952.618
122.73920.61840.94051.33380.10962.07670.0079-0.3382-0.29050.02730.17880.01370.2342-0.2293-0.18670.2556-0.0024-0.0280.11470.09540.1721-35.997-83.20313.082
132.0909-0.41070.19911.0080.54160.463-0.0131-0.0648-0.2445-0.07670.0020.0946-0.0116-0.1170.01110.2787-0.0556-0.01510.14180.05790.2626-45.59-81.412-0.168
1412.0392-0.0106-1.00069.08694.05337.22520.0423-1.0678-0.06570.71530.28490.0277-0.3889-0.5406-0.32720.22270.09150.03490.30290.13880.1618-47.012-72.70419.686
151.74770.16180.06072.9406-0.65660.76850.0523-0.0402-0.07940.08470.00360.0472-0.0324-0.034-0.05590.3059-0.00570.00260.10230.0710.23020.448-45.433-21.372
161.35110.8980.19014.47860.26152.2115-0.07760.0825-0.0005-0.0190.0144-0.29580.02880.14220.06320.2245-0.0257-0.00390.06370.10720.231514.457-37.491-27.919
171.57680.347-0.32691.2443-0.22440.2162-0.04050.2815-0.021-0.20350.0605-0.00010.0512-0.0646-0.020.2527-0.0175-0.02620.08220.0750.19532.97-48.933-30.456
181.75560.7847-0.15031.3069-0.76530.9048-0.02480.20410.22030.03030.08260.1057-0.11080.0003-0.05780.2328-0.0056-0.01160.05320.10490.2541-7.909-34.232-30.913
192.6508-0.4813-0.64941.2239-0.13691.6742-0.10740.3610.3584-0.1063-0.05760.1337-0.13970.16680.1650.2942-0.0665-0.06730.12480.17130.30845.611-23.129-37.718
201.4850.2311-0.18452.70940.50662.2396-0.20840.34310.0817-0.28030.0281-0.21680.09580.18550.18030.2596-0.0690.02990.15470.13330.228915.465-34.608-36.987
2117.9931-0.9846-0.267211.0923-5.537616.3442-0.1702-0.18430.82830.72240.4310.104-0.9027-0.3186-0.26080.3238-0.0578-0.08250.05880.070.281815.127-15.698-24.13
221.9235-0.08650.31871.1339-0.75212.41910.1402-0.0858-0.1414-0.09620.08540.11320.1319-0.0421-0.22560.29410.0019-0.06420.07160.1210.3196-26.562-53.807-37.368
231.0542-0.28880.40330.7724-0.24351.35590.02040.0193-0.0124-0.07560.05770.15870.0507-0.0271-0.07810.2127-0.0214-0.0480.07810.15410.308-32.288-43.896-38.977
240.8342-0.18150.5940.6973-0.37810.91920.07030.2283-0.0176-0.1151-0.06130.02910.08970.2387-0.00890.22160.0103-0.04790.13540.09830.1759-15.347-46.546-44.325
252.3365-1.20190.5821.93960.0221.75050.00460.3390.1438-0.26780.04490.167-0.11990.3056-0.04950.2836-0.0552-0.06580.17590.14810.2148-22.981-34.015-57.669
262.9139-1.2179-2.93272.1211.62015.3564-0.010.18230.0802-0.15260.06070.3542-0.08490.1779-0.05070.2439-0.0319-0.11510.12640.14480.3489-31.92-34.435-50.338
272.74660.8041-0.02410.93360.69782.2445-0.0564-0.16340.260.03620.15340.4202-0.1183-0.132-0.0970.25740.0367-0.0440.14110.17410.4439-38.306-31.561-39.353
286.1995-1.8877-3.86716.43464.479112.97360.18070.4942-0.1368-0.53640.0330.0921-0.03820.0637-0.21370.2745-0.0159-0.14040.14660.12840.2796-36.419-39.491-62.81
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 40
2X-RAY DIFFRACTION2A41 - 163
3X-RAY DIFFRACTION3A164 - 239
4X-RAY DIFFRACTION4A240 - 273
5X-RAY DIFFRACTION5A274 - 295
6X-RAY DIFFRACTION6A296 - 331
7X-RAY DIFFRACTION7A332 - 350
8X-RAY DIFFRACTION8B10 - 50
9X-RAY DIFFRACTION9B51 - 98
10X-RAY DIFFRACTION10B99 - 164
11X-RAY DIFFRACTION11B165 - 243
12X-RAY DIFFRACTION12B244 - 292
13X-RAY DIFFRACTION13B293 - 338
14X-RAY DIFFRACTION14B339 - 350
15X-RAY DIFFRACTION15C10 - 53
16X-RAY DIFFRACTION16C54 - 98
17X-RAY DIFFRACTION17C99 - 162
18X-RAY DIFFRACTION18C163 - 245
19X-RAY DIFFRACTION19C246 - 291
20X-RAY DIFFRACTION20C292 - 342
21X-RAY DIFFRACTION21C343 - 350
22X-RAY DIFFRACTION22D10 - 53
23X-RAY DIFFRACTION23D54 - 154
24X-RAY DIFFRACTION24D155 - 242
25X-RAY DIFFRACTION25D243 - 291
26X-RAY DIFFRACTION26D292 - 314
27X-RAY DIFFRACTION27D315 - 331
28X-RAY DIFFRACTION28D332 - 350

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