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- PDB-3lb0: Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from... -

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Basic information

Entry
Database: PDB / ID: 3lb0
TitleCrystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-Dehydroquinate Dehydratase / aroD / Shikimate Pathway / idp90922 / CSGID / Citrate / 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
CITRIC ACID / FORMIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / 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 typhimurium LT2 with Citrate Bound to the Active Site.
Authors: Minasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: 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 / 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 / _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)60,5635
Polymers60,2032
Non-polymers3603
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-10 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.888, 45.853, 80.816
Angle α, β, γ (deg.)93.95, 101.19, 105.49
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30101.309 Da / Num. of mol.: 2 / Fragment: 3-Dehydroquinate Dehydratase (aroD)
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Protein solution:7.5 mG/mL, 0.01M Comenic acid, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3) Screen solution: JCSG+ (condition 25), 0.2M Sodium Chloride, 0.1M Phosphate-citrate (pH 4.2), ...Details: Protein solution:7.5 mG/mL, 0.01M Comenic acid, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3) Screen solution: JCSG+ (condition 25), 0.2M Sodium Chloride, 0.1M Phosphate-citrate (pH 4.2), 20% w/v PEG8000., 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: Dec 21, 2009 / 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: 1.65→30 Å / Num. all: 56117 / Num. obs: 56117 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 21.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2889 / % possible all: 95.4

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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: 3L2I

3l2i


Resolution: 1.65→26.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.824 / SU ML: 0.063 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20071 2829 5 %RANDOM
Rwork0.16048 ---
all0.16249 53255 --
obs0.16249 53255 93.86 %-
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: 17.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.75 Å2-0.12 Å2
2--2.01 Å2-0.04 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 24 600 4957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224454
X-RAY DIFFRACTIONr_bond_other_d0.0010.022942
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9666087
X-RAY DIFFRACTIONr_angle_other_deg0.89937261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5055602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06524.57186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14915812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1591528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025150
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02872
X-RAY DIFFRACTIONr_mcbond_it1.1451.52835
X-RAY DIFFRACTIONr_mcbond_other0.3371.51144
X-RAY DIFFRACTIONr_mcangle_it1.94824636
X-RAY DIFFRACTIONr_scbond_it2.93931619
X-RAY DIFFRACTIONr_scangle_it4.8334.51451
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 188 -
Rwork0.183 4038 -
obs-4038 95.01 %

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