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- PDB-3s42: Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from... -

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Basic information

Entry
Database: PDB / ID: 3s42
TitleCrystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site
Components3-dehydroquinate dehydratase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM BARREL
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / IMIDAZOLE / MALONIC ACID / NICKEL (II) ION / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLight, S.H. / Minasov, G. / Duban, M.-E. / Halavaty, A.S. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site
Authors: Light, S.H. / Minasov, G. / Duban, M.-E. / Halavaty, A.S. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 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_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.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_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_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_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
B: 3-dehydroquinate dehydratase
A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,06913
Polymers60,2032
Non-polymers86711
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-19 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.562, 72.569, 171.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase


Mass: 30101.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: aroD, STM1358 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P58687, 3-dehydroquinate dehydratase

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Non-polymers , 6 types, 574 molecules

#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 1.89 Å3/Da / Density % sol: 34.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5 M Sodium Chloride, 0.010 M Tris-HCl, Qiagen PACT B2, 0.1 M MIB Buffer (containing 0.025 M Sodium Malonate, 0.037 M Boric Acid, 0.025 M Imidazole), 25% (w/v) PEG 1500, pH 5.5, VAPOR ...Details: 0.5 M Sodium Chloride, 0.010 M Tris-HCl, Qiagen PACT B2, 0.1 M MIB Buffer (containing 0.025 M Sodium Malonate, 0.037 M Boric Acid, 0.025 M Imidazole), 25% (w/v) PEG 1500, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: Beryllium lens
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 81850 / Num. obs: 81850 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.3 / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L20

3l20


Resolution: 1.45→28.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.035 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17527 4091 5 %RANDOM
Rwork0.14352 ---
obs0.14515 77604 99.63 %-
all-77604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.49 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 48 563 4637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224759
X-RAY DIFFRACTIONr_bond_other_d0.0010.023119
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9636494
X-RAY DIFFRACTIONr_angle_other_deg1.05637704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6125643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53124.65200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53315857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8841529
X-RAY DIFFRACTIONr_chiral_restr0.1340.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02927
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_it1.4941.53026
X-RAY DIFFRACTIONr_mcbond_other0.551.51220
X-RAY DIFFRACTIONr_mcangle_it2.29324943
X-RAY DIFFRACTIONr_scbond_it3.39731733
X-RAY DIFFRACTIONr_scangle_it5.2254.51545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 289 -
Rwork0.179 5399 -
obs--96.02 %
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)
10.50540.15630.23380.44580.06010.5066-0.04230.03740.0693-0.0227-0.01070.0299-0.0789-0.00790.0530.0184-0.0011-0.00030.016-0.00840.03797.12379.30735.3344
20.8298-0.18580.00571.28010.12410.9283-0.0318-0.07720.00630.06050.0521-0.0234-0.02870.0703-0.02040.0064-0.0023-0.00080.0326-0.00690.027817.02424.553514.4212
30.3575-0.1005-0.14530.33040.17410.8425-0.0051-0.0018-0.00950.02730.0013-0.00630.07370.00830.00380.00770.0008-0.00020.0002-0.00060.02359.7103-8.11382.4793
40.74450.2750.08281.6782-0.23881.39080.03840.04240.0298-0.0232-0.0417-0.0898-0.03770.04090.00330.02540.00930.00490.0091-0.0020.03610.96076.3723-8.3592
50.59480.17650.21250.2398-0.24690.91650.0221-0.05150.10810.0466-0.02740.0054-0.10770.11550.00530.0945-0.00010.01450.07410.00150.092612.12917.0148-41.4054
61.6481-0.14010.34450.9057-0.12121.22280.0330.15440.06110.0104-0.00070.0574-0.0506-0.0932-0.03230.02870.02810.01750.04760.01490.02761.65315.4063-46.3481
70.4249-0.0057-0.01510.1765-0.18431.47810.0342-0.0366-0.0249-0.029-0.0035-0.00990.1283-0.004-0.03070.0187-0.0055-0.00220.00530.0030.01258.3455-6.9902-35.3454
82.63590.4221.37721.51020.19323.5379-0.08690.0043-0.0535-0.06660.09590.0611-0.3686-0.0631-0.00890.06740.01140.01450.0254-0.00880.03857.28439.5866-24.4425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 44
2X-RAY DIFFRACTION2A45 - 102
3X-RAY DIFFRACTION3A103 - 208
4X-RAY DIFFRACTION4A209 - 252
5X-RAY DIFFRACTION5B-23 - 47
6X-RAY DIFFRACTION6B48 - 91
7X-RAY DIFFRACTION7B92 - 228
8X-RAY DIFFRACTION8B229 - 252

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