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- PDB-3oex: Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) f... -

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Basic information

Entry
Database: PDB / ID: 3oex
TitleCrystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium with close loop conformation.
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
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,6608
Polymers110,5194
Non-polymers1424
Water15,979887
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3304
Polymers55,2592
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-43 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3304
Polymers55,2592
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-46 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.147, 75.757, 94.263
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27629.652 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein: 7.5mGr/mL, 0.5M Sodium Cloride, 0.01M TRIS-HCL pH 8.3, 1mM 3-DHSK; Screen: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate pH 4.6, 25.5% PEG 4000, 15% Glycerol, VAPOR ...Details: Protein: 7.5mGr/mL, 0.5M Sodium Cloride, 0.01M TRIS-HCL pH 8.3, 1mM 3-DHSK; Screen: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate pH 4.6, 25.5% PEG 4000, 15% Glycerol, 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: 1.9→30 Å / Num. all: 69261 / Num. obs: 69261 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3428 / % possible all: 99.7

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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: PDB CODE 3L2I

3l2i


Resolution: 1.9→29.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.183 / SU ML: 0.096 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20366 3507 5.1 %RANDOM
Rwork0.1518 ---
obs0.15443 65729 99.75 %-
all-65729 --
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: 17.986 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.5 Å2
2---0.52 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7649 0 4 887 8540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228136
X-RAY DIFFRACTIONr_bond_other_d0.0010.025363
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.96411081
X-RAY DIFFRACTIONr_angle_other_deg0.88313213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.29651082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05524.411331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.629151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9551554
X-RAY DIFFRACTIONr_chiral_restr0.0870.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
X-RAY DIFFRACTIONr_mcbond_it1.0621.55239
X-RAY DIFFRACTIONr_mcbond_other0.3131.52129
X-RAY DIFFRACTIONr_mcangle_it1.81928518
X-RAY DIFFRACTIONr_scbond_it2.90132897
X-RAY DIFFRACTIONr_scangle_it4.794.52561
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 227 -
Rwork0.188 4777 -
obs-4777 97.66 %
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)
10.3185-0.0789-0.19890.66260.6130.67620.05350.09460.1918-0.03690.01950.0744-0.0214-0.0211-0.0730.04980.0017-0.00040.05430.03960.133220.179812.845336.2761
2-0.1744-0.07230.34193.0881-0.95481.28620.0673-0.04680.07750.11630.00390.26610.0882-0.0928-0.07110.0245-0.00410.02510.0655-0.01290.142114.56111.025349.1904
30.50720.175-0.24370.6875-0.00910.3135-0.0161-0.02940.05490.01330.03720.0650.0761-0.0244-0.02110.04650.0011-0.01480.05320.01280.104315.1372-0.694544.4866
40.7480.0175-0.21820.2405-0.05640.2223-0.13910.0121-0.0876-0.03060.07630.02770.05390.01340.06290.0759-0.0148-0.00050.055-0.00250.08528.0308-7.047335.1958
50.47320.0623-0.37660.35830.01590.3774-0.00470.0650.022-0.00250.0392-0.00890.0167-0.0236-0.03450.0734-0.0138-0.0140.07130.01540.066531.21954.398829.8625
61.86290.1409-0.38692.7396-0.4518-0.405-0.2172-0.43580.16830.22760.2456-0.3943-0.11890.106-0.02840.07490.0224-0.08420.1546-0.03440.055563.430111.805624.3453
70.70350.1459-1.41170.6223-0.38982.6609-0.04490.01910.0245-0.06420.11220.1322-0.02240.0761-0.06730.0899-0.0738-0.02930.08880.02980.023554.071217.14598.4339
80.3933-0.2384-0.45891.8382-0.96980.7798-0.1784-0.0433-0.0137-0.3298-0.0027-0.12320.0780.2520.18110.1055-0.10050.06040.151-0.00090.015964.65648.04316.0024
91.00640.6574-0.1710.69-0.46950.5025-0.10390.024-0.0781-0.05120.0163-0.05980.10360.01970.08760.0843-0.00110.03490.0487-0.01050.073851.0538-3.074818.6012
100.68420.2115-0.6680.5371-0.51172.044-0.00780.0219-0.0005-0.04750.10110.065-0.0508-0.0496-0.09330.0717-0.02120.00430.05060.02820.074145.259912.36819.6598
111.9944-0.6781-0.4031.1062-0.0439-0.0525-0.085-0.12260.1310.26060.0889-0.0997-0.07370.0304-0.00390.093-0.0151-0.06010.1043-0.01380.048148.408910.302269.4048
120.23450.5759-0.43540.3940.18092.3302-0.0147-0.00660.0243-0.0354-0.0090.0439-0.2435-0.06880.02360.09130.031-0.03580.0537-0.01490.079643.333219.72952.0326
130.095-0.1058-0.12710.8377-0.37571.0854-0.02580.01180.0135-0.021-0.0288-0.0667-0.00790.13640.05460.0160.0003-0.01720.09940.00620.087352.92136.316750.5307
140.6272-0.210.04610.2256-0.17750.3650.0074-0.0057-0.0723-0.0198-0.0126-0.030.09970.00370.00520.07760.0243-0.01480.07760.00430.064339.5594-6.768862.8984
150.5570.0847-0.39120.4059-0.02960.4860.0085-0.0211-0.0295-0.00190.0160.0566-0.04820.0292-0.02450.0740.0159-0.0180.0671-0.00780.064535.31768.258464.8026
162.53150.748-1.11161.03120.58711.2630.06810.179-0.0134-0.2565-0.1582-0.0603-0.2685-0.33180.09010.07870.06380.00090.1481-0.01720.00267.77668.674671.8676
17-0.0915-0.5436-0.90410.86770.73334.09630.02220.01750.00890.02210.0388-0.1579-0.1944-0.1842-0.0610.09430.00780.01760.0757-0.02340.036410.773315.601691.284
18-2.0705-0.2373-1.27721.41972.18914.3172-0.03460.33610.12730.3791-0.5668-0.17070.3166-0.75160.60140.0704-0.08210.0020.1363-0.05960.08594.03137.428791.4
191.0867-0.2015-0.65650.44851.06660.8432-0.03570.12780.0760.1923-0.16860.06540.2964-0.09040.20430.1299-0.06280.04910.0548-0.01770.044414.207-5.302980.2289
201.61220.2982-0.891.03620.21561.3287-0.019-0.155-0.015-0.01110.053-0.0168-0.10470.0331-0.0340.07640.02270.02340.0669-0.00980.047321.211610.6275.5128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 46
2X-RAY DIFFRACTION2A47 - 71
3X-RAY DIFFRACTION3A72 - 131
4X-RAY DIFFRACTION4A132 - 189
5X-RAY DIFFRACTION5A190 - 252
6X-RAY DIFFRACTION6B-2 - 11
7X-RAY DIFFRACTION7B12 - 54
8X-RAY DIFFRACTION8B55 - 138
9X-RAY DIFFRACTION9B139 - 217
10X-RAY DIFFRACTION10B218 - 252
11X-RAY DIFFRACTION11C-2 - 19
12X-RAY DIFFRACTION12C20 - 45
13X-RAY DIFFRACTION13C46 - 139
14X-RAY DIFFRACTION14C140 - 196
15X-RAY DIFFRACTION15C197 - 252
16X-RAY DIFFRACTION16D-2 - 19
17X-RAY DIFFRACTION17D20 - 57
18X-RAY DIFFRACTION18D58 - 113
19X-RAY DIFFRACTION19D114 - 212
20X-RAY DIFFRACTION20D213 - 252

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