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- PDB-3l2i: 1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydrata... -

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Basic information

Entry
Database: PDB / ID: 3l2i
Title1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2.
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-dehydroquinate dehydratase / aroD / Shikimate pathway / idp90922 / csgid / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Schiff base / Structural Genomics / Center for Structural Genomics of Infectious Diseases
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
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochemistry / Year: 2011
Title: A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding.
Authors: Light, S.H. / Minasov, G. / Shuvalova, L. / Peterson, S.N. / Caffrey, M. / Anderson, W.F. / Lavie, A.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2273
Polymers60,2032
Non-polymers241
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-25 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.919, 76.909, 171.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein solution: 7.5 mG/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2, drop D3; 0.2M Magnesium Chloride, 20% PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 42861 / Num. obs: 42861 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2081 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQN

1gqn


Resolution: 1.85→28.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.727 / SU ML: 0.085 / Isotropic thermal model: REFINED INDIVIDUALLY / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21384 2141 5 %RANDOM
Rwork0.16753 ---
all0.16982 40646 --
obs0.16982 40646 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.71 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 1 443 4339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224198
X-RAY DIFFRACTIONr_bond_other_d0.0010.022759
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9625722
X-RAY DIFFRACTIONr_angle_other_deg0.92636809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5885559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6424.713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94215764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4831525
X-RAY DIFFRACTIONr_chiral_restr0.10.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02806
X-RAY DIFFRACTIONr_mcbond_it1.2011.52679
X-RAY DIFFRACTIONr_mcbond_other0.3311.51088
X-RAY DIFFRACTIONr_mcangle_it2.15424368
X-RAY DIFFRACTIONr_scbond_it3.30931519
X-RAY DIFFRACTIONr_scangle_it5.5624.51351
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 162 -
Rwork0.21 2848 -
obs-2848 98.56 %

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