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- PDB-4h3d: 1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Deh... -

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Entry
Database: PDB / ID: 4h3d
Title1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.
Components3-dehydroquinate dehydratase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM Barrel / Aldolase class I / 3-dehydroquinate dehydratase activity
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-SHL / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Duban, M.-E. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.
Authors: Minasov, G. / Light, S.H. / Shuvalova, L. / Duban, M.-E. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 20, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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

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)118,12215
Polymers116,7524
Non-polymers1,37011
Water14,718817
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1388
Polymers58,3762
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9857
Polymers58,3762
Non-polymers6095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.275, 138.688, 66.315
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 29188.055 Da / Num. of mol.: 4 / Fragment: Type I 3-dehydroquinate Dehydratase (aroD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: aroD, CD630_22170 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q186A6, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 828 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SHL / 5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid / Comenic acid


Mass: 170.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O5
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.5mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3. Screen: 0.1M MES pH 6.5, 25% (v/v) PEG 550 MME. 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: Nov 25, 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: 1.95→30 Å / Num. all: 79221 / Num. obs: 79221 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3903 / % possible all: 99.6

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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 ENTRY 3JS3

3js3


Resolution: 1.95→27.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.229 / SU ML: 0.095
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19936 4014 5.1 %RANDOM
Rwork0.15561 ---
all0.15788 74846 --
obs0.15788 74846 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.372 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.21 Å2
2--0.5 Å2-0 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8036 0 94 817 8947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228661
X-RAY DIFFRACTIONr_bond_other_d0.0010.026060
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.99211687
X-RAY DIFFRACTIONr_angle_other_deg1.9743.00114928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.46951093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27425.109368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.365151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1561548
X-RAY DIFFRACTIONr_chiral_restr0.0850.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021605
X-RAY DIFFRACTIONr_mcbond_it1.2381.55304
X-RAY DIFFRACTIONr_mcbond_other0.421.52132
X-RAY DIFFRACTIONr_mcangle_it2.09128688
X-RAY DIFFRACTIONr_scbond_it3.47433357
X-RAY DIFFRACTIONr_scangle_it5.4694.52999
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 289 -
Rwork0.187 5442 -
obs-5442 99.12 %
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)
11.7920.18070.50611.40970.30121.6393-0.1009-0.04030.18410.02540.0586-0.0802-0.16660.05780.04230.0284-0.0077-0.00850.0176-0.01580.031347.9501-8.037371.379
21.71860.51140.32622.17210.22791.99750.046-0.2104-0.08950.1890.0558-0.19670.13030.1329-0.10180.0452-0.0084-0.03020.0892-0.01260.038352.8015-19.051275.5799
30.81350.46950.21710.4646-0.61053.1170.0691-0.0037-0.23660.0058-0.0408-0.14290.24120.1756-0.02840.04490.0123-0.01230.0382-0.01070.077348.2958-31.368960.134
41.38460.02190.16310.8166-0.07611.08650.06080.0556-0.0661-0.0262-0.05730.01860.07560.0053-0.00350.0221-0.0031-0.01220.0207-0.01260.024641.4365-24.387157.2291
57.0180.52841.91714.39453.23044.8981-0.2980.26920.4562-0.77630.0095-0.0091-0.69530.0420.28860.22770.0223-0.04710.07980.02170.06238.5469-8.941456.0093
62.3647-0.6838-0.28264.35152.51064.31050.06320.28450.2223-0.20580.0831-0.7276-0.2820.3138-0.14630.0563-0.0450.0040.08840.03760.159338.4076-11.115829.2644
72.1905-0.07980.7472.3853-0.01132.0313-0.0529-0.05650.20450.02990.03030.1627-0.2043-0.28830.02260.03230.0233-0.00090.07860.0210.040516.9402-8.071227.8481
81.6004-0.0259-0.42522.4632-0.37733.1020.03140.23-0.055-0.32460.05030.05380.0009-0.0637-0.08170.0488-0.0155-0.01540.06780.01550.020724.1508-17.644718.3828
91.050.4242-0.06690.9952-0.1732.69420.106-0.0546-0.12430.063-0.0822-0.11890.25730.0572-0.02380.0667-0.0234-0.04150.02530.02060.059131.8151-26.676536.5075
105.6472-1.28311.63363.6352-0.70495.2266-0.0976-0.26020.15160.4456-0.0152-0.0892-0.3619-0.28990.11280.184-0.0502-0.05470.06240.03170.070833.1066-10.373543.4721
111.9994-0.0044-0.47761.37980.20131.6694-0.08720.0529-0.2368-0.02640.0468-0.05760.15060.06350.04040.02880.00660.00720.0284-0.02030.036948.08837.646328.3699
123.0054-0.1268-0.56951.65880.46872.18450.01330.1472-0.0383-0.14130.0813-0.2354-0.06960.1198-0.09470.02780.01590.02120.0628-0.01850.037153.973114.404824.9102
134.16920.58911.82064.46350.49666.0745-0.01420.39820.2271-0.4916-0.0008-0.0654-0.32730.27870.0150.11520.02690.04950.11370.01810.055349.615424.287120.9443
141.2708-0.1341-0.02451.0033-0.10061.12960.0525-0.04020.10410.0242-0.053-0.0266-0.07450.06770.00060.02690.00280.01660.0278-0.01020.031643.779225.438541.1389
1515.9641-3.4964-2.55145.61123.64976.5177-0.4755-0.4292-0.34970.76930.07440.07050.74750.04110.40120.2489-0.03870.05780.07660.03190.067338.11857.912443.9072
162.59631.3862-0.71574.78861.88193.95670.1406-0.2942-0.31870.29120.1031-0.73940.22340.4373-0.24370.08030.052-0.00690.10110.03120.151638.713110.81570.3327
172.09130.3488-0.87282.0564-0.0482.0795-0.08230.0718-0.1908-0.03260.03670.13410.246-0.26910.04560.0456-0.01950.00960.07640.02150.042716.93947.435171.669
181.4920.30180.2141.3267-0.24022.81330.0607-0.22130.05640.31830.01170.02270.0113-0.0675-0.07240.08460.01580.01630.07170.02040.033124.115716.983881.1292
190.8433-0.223-0.161.1333-0.35332.70040.10820.02590.1111-0.0524-0.0867-0.1099-0.26370.0522-0.02150.07180.02670.04620.02970.02010.064631.84725.912362.9503
206.01361.9683-1.66723.1302-0.60835.0539-0.12420.2825-0.208-0.33730.0419-0.24450.292-0.250.08240.15160.04730.06390.06390.0350.072733.63619.837156.2532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION2A72 - 142
3X-RAY DIFFRACTION3A143 - 164
4X-RAY DIFFRACTION4A165 - 224
5X-RAY DIFFRACTION5A225 - 255
6X-RAY DIFFRACTION6B1 - 21
7X-RAY DIFFRACTION7B22 - 101
8X-RAY DIFFRACTION8B102 - 139
9X-RAY DIFFRACTION9B140 - 213
10X-RAY DIFFRACTION10B214 - 254
11X-RAY DIFFRACTION11C1 - 68
12X-RAY DIFFRACTION12C69 - 118
13X-RAY DIFFRACTION13C119 - 140
14X-RAY DIFFRACTION14C141 - 226
15X-RAY DIFFRACTION15C227 - 255
16X-RAY DIFFRACTION16D0 - 21
17X-RAY DIFFRACTION17D22 - 101
18X-RAY DIFFRACTION18D102 - 139
19X-RAY DIFFRACTION19D140 - 213
20X-RAY DIFFRACTION20D214 - 254

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