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- PDB-4hso: Crystal structure of S213G variant DAH7PS from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 4hso
TitleCrystal structure of S213G variant 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 / identical protein 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 / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_ref_seq_dif / 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_label_asym_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_ref_seq_dif.details / _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)156,34516
Polymers154,7284
Non-polymers1,61712
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-94 kcal/mol
Surface area43960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.523, 136.995, 76.212
Angle α, β, γ (deg.)90.000, 96.630, 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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA8 - 3498 - 349
21ASPASPARGARGBB8 - 3498 - 349
12PROPROARGARGAA6 - 3496 - 349
22PROPROARGARGCC6 - 3496 - 349
13PROPROARGARGAA6 - 3496 - 349
23PROPROARGARGDD6 - 3496 - 349
14ASPASPARGARGBB8 - 3498 - 349
24ASPASPARGARGCC8 - 3498 - 349
15ASPASPARGARGBB8 - 3498 - 349
25ASPASPARGARGDD8 - 3498 - 349
16TYRTYRALAALACC5 - 3505 - 350
26TYRTYRALAALADD5 - 3505 - 350

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: 38682.109 Da / Num. of mol.: 4 / Mutation: S213G
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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
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: 2.1→19.571 Å / Num. all: 86154 / Num. obs: 86154 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rsym value: 0.047 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.213.80.3931.947490126590.39399.7
2.21-2.353.70.2842.543093117540.28497.9
2.35-2.513.80.1824.242460112600.18299.7
2.51-2.713.70.128638924104260.12899
2.71-2.973.80.0839.43644596470.08399.9
2.97-3.323.80.0515.23313387880.0599.6
3.32-3.833.70.03122.82741775110.03197.1
3.83-4.73.70.02427.62338763760.02497.4
4.7-6.643.70.02131.21888650570.02199.3
6.64-19.5713.60.01735965026760.01794.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HSN

4hsn


Resolution: 2.1→19.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2274 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8301 / SU B: 11.901 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2333 / SU Rfree: 0.1896 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 4334 5 %RANDOM
Rwork0.204 ---
obs0.2059 86108 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.89 Å2 / Biso mean: 39.6033 Å2 / Biso min: 20.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0 Å2-0.1 Å2
2--2.38 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10495 0 96 257 10848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910807
X-RAY DIFFRACTIONr_bond_other_d0.0090.0210308
X-RAY DIFFRACTIONr_angle_refined_deg1.611.96614647
X-RAY DIFFRACTIONr_angle_other_deg1.431323676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2151382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98824.021475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.868151814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.261573
X-RAY DIFFRACTIONr_chiral_restr0.0930.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112350
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022407
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms
11A204890.1
12B204890.1
21A204230.12
22C204230.12
31A210330.1
32D210330.1
41B199870.12
42C199870.12
51B203290.1
52D203290.1
61C204750.12
62D204750.12
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 335 -
Rwork0.273 6082 -
all-6417 -
obs--99.74 %
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)
12.06140.3066-0.07620.5859-0.61960.92130.04680.09040.2601-0.0124-0.0398-0.0608-0.0849-0.0238-0.00690.1132-0.0075-0.01860.10390.05310.2411-5.824-70.092-15.579
21.64550.2037-0.00911.77490.52390.9453-0.02790.1216-0.1516-0.11-0.0187-0.11810.10250.13360.04660.05560.0095-0.00130.06530.01080.23714.841-90.181-10.36
310.5679-1.0828-5.36650.11480.55142.72620.2158-0.17910.3094-0.0089-0.0368-0.0154-0.12480.0804-0.1790.1594-0.07240.04720.28740.03310.2667-7.514-75.6572.988
41.49910.29250.30741.8107-0.07470.7456-0.0538-0.01320.120.034-0.02770.0072-0.0433-0.02030.08140.0306-0.0111-0.01620.07330.02480.2361-1.237-74.357-10.172
51.0423-0.13650.0720.9456-0.4660.55580.01940.0361-0.0939-0.05910.06170.12210.0557-0.049-0.08110.0678-0.0373-0.03360.0758-0.0210.2505-15.633-87.583-9.543
61.75140.13860.69781.52350.23752.03090.0511-0.1139-0.25450.0117-0.04830.00020.21960.046-0.00280.0768-0.0158-0.00780.04270.00470.3171-5.808-100.529-2.119
71.80960.22670.03011.42910.25271.880.0572-0.1334-0.20670.0346-0.054-0.15550.0980.1628-0.00320.04450.0041-0.00770.10520.05280.26246.87-91.2270.197
80.60940.9149-0.065710.2619-1.45290.26740.4222-0.15830.2309-1.9291-0.4742-0.85610.41080.08230.0521.07310.05230.3110.1722-0.08970.5983-16.15-77.145-25.525
91.4201-0.0224-0.77630.6591-0.3732.07020.0212-0.07460.13960.09550.12450.1207-0.0602-0.2593-0.14570.02080.0055-0.0170.11970.05320.2568-40.307-66.032-0.471
101.02880.4685-0.75560.2565-0.36820.5713-0.1197-0.1687-0.3678-0.1703-0.0902-0.08790.14560.14910.20990.34770.0386-0.10180.25950.02510.4603-32.637-79.969-13.701
111.6783-0.0803-0.06840.8741-0.76463.4625-0.05610.13080.04830.01410.1234-0.05720.2292-0.0625-0.06730.0386-0.0384-0.0340.13180.05250.2991-35.261-68.891-12.107
121.0251-0.0686-0.23590.6485-0.44720.83190.005-0.1189-0.03010.02190.0084-0.00860.0321-0.0137-0.01330.0337-0.0192-0.03950.10840.00880.2317-24.104-73.4982.312
131.8155-0.06850.76221.06970.20221.1185-0.0504-0.1196-0.23250.0150.10.08530.173-0.1065-0.04960.0651-0.0524-0.01690.12760.06660.2416-40.492-82.0795.651
148.09690.19472.64184.71452.771412.8273-0.0438-0.81760.04890.25170.11870.1709-0.2341-0.583-0.07480.0370.03640.05870.28460.14720.2426-48.19-74.47716.246
1515.0771-1.13875.40871.6482-0.19512.02040.7960.3987-0.7588-0.128-0.43660.21480.3715-0.0064-0.35940.205-0.1367-0.16390.33250.02780.3677-17.562-62.488-39.931
161.2040.7365-0.02371.6612-0.54790.64560.0098-0.00840.00970.0458-0.0436-0.1457-0.06520.12760.03380.0253-0.032-0.02360.07640.03660.221410.073-38.912-23.002
171.5906-0.87674.64216.6523-8.729719.7546-0.3719-0.24370.1588-0.9760.0262-0.08360.2486-0.80180.34570.4646-0.0184-0.14940.67550.23570.29981.734-48.663-39.387
182.1610.5994-0.65312.94110.13120.33980.01220.1882-0.1546-0.20140.0223-0.00070.0296-0.0557-0.03450.0728-0.0138-0.03020.10760.03740.2363.631-48.769-27.255
191.37290.5171-0.16810.9376-0.45370.6861-0.00490.18510.1731-0.02380.09590.0784-0.04740.0142-0.0910.0388-0.0024-0.01440.10330.06060.2567-8.442-35.006-30.315
2011.9941-1.2255-10.55062.91031.897410.62860.26260.30520.6343-0.32290.11860.3582-0.4805-0.1475-0.38120.1934-0.0661-0.16340.09990.19010.39130.944-17.726-38.604
211.38340.0523-0.31361.4706-0.861.7401-0.12960.2730.1765-0.174-0.0161-0.1376-0.01740.12250.14570.0769-0.0866-0.01480.14920.07810.252412.508-28.864-35.821
222.18660.4203-0.3011.0216-0.56120.56560.1097-0.1638-0.04190.0062-0.0084-0.00990.1012-0.1193-0.10130.1021-0.0093-0.05260.13920.07580.2927-23.512-52.449-33.561
231.0502-0.23670.3970.7078-0.24722.01710.0450.00090.0456-0.02380.01540.0433-0.0002-0.0193-0.06040.0164-0.0135-0.04260.11060.09340.2743-32.562-43.544-39.747
240.4525-0.02410.52830.7137-0.46621.32990.0220.1510.0014-0.0854-0.0244-0.01660.03930.1710.00250.0236-0.0008-0.03730.15540.05670.2085-15.64-46.712-43.408
2515.8687-10.3861-2.130210.09475.15994.5944-0.15850.62160.1869-0.50750.1775-0.0861-0.64980.6572-0.0190.1523-0.05530.00490.37770.10790.1441-17.486-33.168-62.125
261.7914-1.2921-0.60721.56160.48061.8180.05030.14120.1094-0.18050.05130.0689-0.20340.1864-0.10160.0875-0.0411-0.06770.14920.09870.2162-26.589-34.63-55.573
272.5941-1.2086-1.32111.75720.46680.7376-0.0936-0.23570.28210.16970.17110.2634-0.01270.0726-0.07750.12220.0677-0.0760.22480.0250.4325-37.3-30.281-38.072
285.2496-2.6819-4.34315.6343.726210.28870.24590.5469-0.0843-0.4844-0.1094-0.0417-0.0972-0.0983-0.13640.12620.0143-0.10950.18520.09360.2558-36.147-39.369-62.609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 43
2X-RAY DIFFRACTION2A44 - 97
3X-RAY DIFFRACTION3A98 - 108
4X-RAY DIFFRACTION4A109 - 162
5X-RAY DIFFRACTION5A163 - 249
6X-RAY DIFFRACTION6A250 - 302
7X-RAY DIFFRACTION7A303 - 350
8X-RAY DIFFRACTION8B8 - 17
9X-RAY DIFFRACTION9B18 - 95
10X-RAY DIFFRACTION10B96 - 115
11X-RAY DIFFRACTION11B116 - 149
12X-RAY DIFFRACTION12B150 - 249
13X-RAY DIFFRACTION13B250 - 333
14X-RAY DIFFRACTION14B334 - 350
15X-RAY DIFFRACTION15C5 - 17
16X-RAY DIFFRACTION16C18 - 96
17X-RAY DIFFRACTION17C97 - 113
18X-RAY DIFFRACTION18C114 - 162
19X-RAY DIFFRACTION19C163 - 241
20X-RAY DIFFRACTION20C242 - 254
21X-RAY DIFFRACTION21C255 - 350
22X-RAY DIFFRACTION22D5 - 51
23X-RAY DIFFRACTION23D52 - 149
24X-RAY DIFFRACTION24D150 - 242
25X-RAY DIFFRACTION25D243 - 253
26X-RAY DIFFRACTION26D254 - 309
27X-RAY DIFFRACTION27D310 - 331
28X-RAY DIFFRACTION28D332 - 350

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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