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- PDB-4ixx: Crystal structure of S213G variant DAH7PS without Tyr bound from ... -

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Basic information

Entry
Database: PDB / ID: 4ixx
TitleCrystal structure of S213G variant DAH7PS without Tyr bound from Neisseria meningitidis
Components3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
KeywordsTRANSFERASE / DAHP / DAHPS / DAH7PS / TIM BARREL / ALLOSTERIC REGULATION / AROMATIC BIOSYNTHESIS / SHIKIMATE PATHWAY / TIM-BARREL
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
: / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 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_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_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)155,62115
Polymers154,7284
Non-polymers89211
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-193 kcal/mol
Surface area45510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.064, 132.432, 75.028
Angle α, β, γ (deg.)90.000, 95.720, 90.000
Int Tables number4
Space group name H-MP1211

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
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, temperature 293.15K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.931→74.654 Å / Num. all: 55141 / Num. obs: 55141 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.4-2.473.80.4862.717148451899.9
10.18-19.593.50.0252226364285.4

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Processing

Software
NameVersionClassificationNB
Aimless0.1.30data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HSO

4hso


Resolution: 2.4→19.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2002 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8591 / SU B: 18.025 / SU ML: 0.195 / SU R Cruickshank DPI: 0.4943 / SU Rfree: 0.2493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.494 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 3384 6.1 %RANDOM
Rwork0.1914 ---
obs0.1935 55115 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.18 Å2 / Biso mean: 48.9273 Å2 / Biso min: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0 Å2-0.05 Å2
2--2.18 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10404 0 39 100 10543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910624
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210243
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.96514377
X-RAY DIFFRACTIONr_angle_other_deg1.24323540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96251357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11623.966464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.357151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4251574
X-RAY DIFFRACTIONr_chiral_restr0.0790.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112071
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022359
X-RAY DIFFRACTIONr_mcbond_it1.3971.8865440
X-RAY DIFFRACTIONr_mcbond_other1.3951.8855439
X-RAY DIFFRACTIONr_mcangle_it2.2482.8226793
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 223 -
Rwork0.274 3811 -
all-4034 -
obs--99.95 %
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)
19.22791.2451-3.182.0446-2.94115.31960.14580.34281.9284-0.64420.1371-0.32530.5471-0.2294-0.28290.4774-0.02620.23570.27070.04390.8977-2.312-68.721-16.795
21.81260.1-0.06171.3654-0.7020.9865-0.08510.0945-0.0152-0.38890.0238-0.07630.32940.00350.06130.2763-0.05040.01840.1617-0.0210.1536-5.112-81.02-9.523
35.20664.14522.98094.84752.16176.959-0.1779-0.1643-0.7114-0.6394-0.0462-0.24420.6781-0.38650.22410.415-0.07130.02730.15040.02770.4386-12.003-98.694-2.618
46.11755.93721.25736.04463.027113.6275-0.1039-0.5025-0.17380.0561-0.4121-0.0330.24710.26820.5160.37290.05550.10790.24880.16690.37020.221-93.3898.123
52.81741.3278-0.11742.95170.18341.9498-0.0824-0.2079-0.5545-0.4475-0.1466-0.44510.41970.1740.2290.26520.06150.0630.20540.08570.30964.529-92.426-0.389
61.3686-0.0175-0.46571.7555-1.79633.6888-0.01140.06860.3222-0.030.53720.37130.0054-0.7014-0.52580.0153-0.0127-0.00010.39510.13830.328-38.518-64.493-2.1
70.0219-0.003-0.00960.00230.00030.00740.05990.13540.0564-0.0365-0.003-0.03170.0122-0.0705-0.05690.83370.0980.12431.01710.1341.1405-30.303-80.53-9.752
83.51350.3566-2.20110.8233-1.50156.0818-0.13760.24690.2059-0.36150.34410.160.5688-0.4043-0.20650.1966-0.1585-0.07140.3040.13660.2608-34.008-68.479-12.702
92.38840.4372-0.66221.7852-1.80962.3701-0.1079-0.23420.0244-0.1270.39540.2120.3287-0.49-0.28750.1206-0.0744-0.03060.3390.05990.167-32.497-75.2335.067
1018.09676.11914.017719.97750.731511.76381.4091-0.97440.04682.0997-1.2960.50510.6644-0.5687-0.11310.6992-0.02520.28810.80850.0480.4662-44.882-68.85123.702
112.16060.5832-0.05494.3111-0.80221.39250.1357-0.2266-0.2977-0.0749-0.3823-0.69690.04340.15710.24660.08270.00350.01530.29710.14220.28578.669-39.359-24.128
120.20561.5871-0.532212.9123-4.28711.4347-0.14240.091-0.0226-1.39120.24460.2190.4628-0.1927-0.10210.68040.0986-0.05381.06030.17230.64191.156-45.074-40.694
132.43940.3169-0.54783.4272-0.81190.28880.1086-0.0867-0.3505-0.3891-0.2351-0.2120.06850.04870.12640.15020.01050.03340.21870.10180.26953.595-47.181-28.173
142.98131.0264-0.70432.6913-1.41321.43530.04540.19990.2863-0.1576-0.03740.0082-0.0767-0.0487-0.0080.18630.0110.02020.24490.04830.1954-5.19-29.223-32.018
153.05021.2588-1.35975.7084-1.2313.477-0.04250.17270.1213-0.7134-0.4977-0.94780.09150.41740.54020.14040.04250.18030.2790.22910.447415.645-28.654-36.051
163.44420.26231.19751.166-0.96073.62690.2268-0.0674-0.3491-0.1575-0.1724-0.03470.46950.1875-0.05440.25240.0791-0.05480.23710.01130.3258-25.84-51.546-36.649
173.1679-0.26531.61872.7022.88076.6993-0.04850.08780.1984-0.07510.01950.34920.2227-0.12450.02890.28010.0101-0.02080.29040.08240.2679-37.974-40.6-44.832
181.9070.05621.05040.0969-0.20841.32810.11140.0619-0.0757-0.0452-0.0430.04490.06260.1927-0.06840.21540.0022-0.00510.20980.0290.1933-25.56-42.62-38
192.5750.61851.05552.1106-2.14473.37560.30990.6348-0.3591-0.0764-0.1245-0.02210.30880.5819-0.18540.22460.1434-0.00250.4224-0.05330.243-10.95-49.604-41.655
203.5147-0.16491.18431.47291.25512.8211-0.18620.75640.5787-0.3430.06830.1744-0.28250.65290.11790.248-0.0311-0.05130.42080.16240.227-28.356-32.855-53.169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 41
2X-RAY DIFFRACTION2A42 - 239
3X-RAY DIFFRACTION3A240 - 271
4X-RAY DIFFRACTION4A272 - 285
5X-RAY DIFFRACTION5A286 - 350
6X-RAY DIFFRACTION6B12 - 96
7X-RAY DIFFRACTION7B97 - 105
8X-RAY DIFFRACTION8B106 - 153
9X-RAY DIFFRACTION9B154 - 344
10X-RAY DIFFRACTION10B345 - 350
11X-RAY DIFFRACTION11C11 - 96
12X-RAY DIFFRACTION12C97 - 108
13X-RAY DIFFRACTION13C109 - 165
14X-RAY DIFFRACTION14C166 - 275
15X-RAY DIFFRACTION15C276 - 350
16X-RAY DIFFRACTION16D9 - 53
17X-RAY DIFFRACTION17D54 - 83
18X-RAY DIFFRACTION18D84 - 192
19X-RAY DIFFRACTION19D193 - 228
20X-RAY DIFFRACTION20D229 - 350

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