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- PDB-3o1n: 1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroqui... -

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Basic information

Entry
Database: PDB / ID: 3o1n
Title1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium
Components3-dehydroquinate dehydratase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / dehydratase
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: 1.03 Å
AuthorsLight, S.H. / Minasov, G. / 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
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,2217
Polymers60,0892
Non-polymers1335
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-51 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.433, 46.476, 55.790
Angle α, β, γ (deg.)104.23, 97.50, 98.70
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30044.258 Da / Num. of mol.: 2 / Mutation: Q236A
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 (Magic) / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 1.85 Å3/Da / Density % sol: 33.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M Tris, pH 8.5, 25% (w/v) 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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.03→30 Å / Num. all: 196964 / Num. obs: 196964 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.7 / Num. unique all: 8952 / % possible all: 84.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L2I

3l2i


Resolution: 1.03→26.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.763 / SU ML: 0.018
Isotropic thermal model: Anisotropically refined individual B-factors
Cross valid method: THROUGHOUT / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16161 9868 5 %RANDOM
Rwork0.14024 ---
all0.14132 187094 --
obs0.14132 187094 92.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.933 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20.61 Å2-0.79 Å2
2--1.22 Å2-0.89 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.03→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 5 775 4565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224184
X-RAY DIFFRACTIONr_bond_other_d0.0010.022771
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9675715
X-RAY DIFFRACTIONr_angle_other_deg0.88636847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15124.477172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69715773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1061528
X-RAY DIFFRACTIONr_chiral_restr0.090.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02807
X-RAY DIFFRACTIONr_mcbond_it1.6961.52674
X-RAY DIFFRACTIONr_mcbond_other0.6381.51083
X-RAY DIFFRACTIONr_mcangle_it2.48224366
X-RAY DIFFRACTIONr_scbond_it3.41931510
X-RAY DIFFRACTIONr_scangle_it4.9224.51337
X-RAY DIFFRACTIONr_rigid_bond_restr1.44536955
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 666 -
Rwork0.175 12586 -
obs--84.55 %

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