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- PDB-3l9c: The Crystal Structure of smu.777 from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l9c
TitleThe Crystal Structure of smu.777 from Streptococcus mutans UA159
Components3-dehydroquinate dehydratase
KeywordsLYASE / aroD / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Schiff base
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 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 speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSu, X.-D. / Huang, Y.H. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.777 from Streptococcus mutans UA159
Authors: Su, X.-D. / Huang, Y.H. / Liu, X.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)58,7162
Polymers58,7162
Non-polymers00
Water2,612145
1
A: 3-dehydroquinate dehydratase


Theoretical massNumber of molelcules
Total (without water)29,3581
Polymers29,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-dehydroquinate dehydratase


Theoretical massNumber of molelcules
Total (without water)29,3581
Polymers29,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.280, 62.940, 65.070
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-dehydroquinate dehydratase / smu.777 / 3-dehydroquinase / Type I DHQase


Mass: 29358.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.777 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DUW4, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M Magnesium Chloride hexahydrate, 0.1M HEPES pH7.5, 30% PEGMME550, 0.01M Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97156 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97156 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. all: 66520 / Num. obs: 66453 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 20.77 Å2
Reflection shellResolution: 1.54→1.56 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ocz

2ocz


Resolution: 1.6→28.888 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.788 / SU ML: 0.23 / σ(F): 1.89 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 3019 5.12 %
Rwork0.2215 55895 -
obs0.223 58914 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.293 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 80.89 Å2 / Biso mean: 27.333 Å2 / Biso min: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.095 Å20 Å2-7.788 Å2
2--5.27 Å20 Å2
3----5.365 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 0 145 3681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043607
X-RAY DIFFRACTIONf_angle_d0.9074897
X-RAY DIFFRACTIONf_dihedral_angle_d17.8751308
X-RAY DIFFRACTIONf_chiral_restr0.064570
X-RAY DIFFRACTIONf_plane_restr0.003628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.33591350.27532573X-RAY DIFFRACTION100
1.625-1.65160.29921510.25372467X-RAY DIFFRACTION100
1.6516-1.68010.2841580.24822548X-RAY DIFFRACTION100
1.6801-1.71070.32911360.25152514X-RAY DIFFRACTION100
1.7107-1.74360.27531370.24642547X-RAY DIFFRACTION100
1.7436-1.77920.29411250.24912530X-RAY DIFFRACTION100
1.7792-1.81780.25571300.24432532X-RAY DIFFRACTION100
1.8178-1.86010.30861210.2412552X-RAY DIFFRACTION100
1.8601-1.90660.30641390.24642542X-RAY DIFFRACTION100
1.9066-1.95820.25811240.24272521X-RAY DIFFRACTION100
1.9582-2.01580.31651410.24182529X-RAY DIFFRACTION100
2.0158-2.08080.2781410.24422511X-RAY DIFFRACTION100
2.0808-2.15520.24181650.23442528X-RAY DIFFRACTION100
2.1552-2.24140.21271300.22472531X-RAY DIFFRACTION100
2.2414-2.34340.25351500.2292525X-RAY DIFFRACTION100
2.3434-2.46690.27261370.23032552X-RAY DIFFRACTION100
2.4669-2.62130.26581480.23512547X-RAY DIFFRACTION100
2.6213-2.82360.27871240.2372558X-RAY DIFFRACTION100
2.8236-3.10740.27041220.24112573X-RAY DIFFRACTION100
3.1074-3.55640.2321470.21862523X-RAY DIFFRACTION100
3.5564-4.4780.2051420.18192583X-RAY DIFFRACTION100
4.478-28.89290.2021160.17882609X-RAY DIFFRACTION98

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