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- PDB-2bt4: Type II Dehydroquinase inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 2bt4
TitleType II Dehydroquinase inhibitor complex
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / SHIKIMATE PATHWAY / DEHYDROQUINATE / AMINO-ACID BIOSYNTHESIS / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CA2 / PHOSPHATE ION / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsToscano, M.D. / Stewart, K.A. / Coggins, J.R. / Lapthorn, A.J. / Abell, C.
Citation
Journal: Org.Biomol.Chem. / Year: 2005
Title: Rational Design of New Bifunctional Inhibitors of Type II Dehydroquinase.
Authors: Toscano, M.D. / Stewart, K.A. / Coggins, J.R. / Lapthorn, A.J. / Abell, C.
#1: Journal: Structure / Year: 2002
Title: The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor
Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Frederickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionMay 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
G: 3-DEHYDROQUINATE DEHYDRATASE
H: 3-DEHYDROQUINATE DEHYDRATASE
I: 3-DEHYDROQUINATE DEHYDRATASE
J: 3-DEHYDROQUINATE DEHYDRATASE
K: 3-DEHYDROQUINATE DEHYDRATASE
L: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,10744
Polymers200,41012
Non-polymers5,69832
Water31,1841731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)196.616, 196.487, 240.626
Angle α, β, γ (deg.)65.91, 65.91, 90.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 2350
2112B2 - 2350
3112C2 - 2350
4112D2 - 2350
5112E2 - 2350
6112F2 - 2350
7112G2 - 2350
8112H2 - 2350
9112I2 - 2350
10112J2 - 2350
11112K2 - 2350
12112L2 - 2350

NCS oper:
IDCodeMatrixVector
1given(1, 0.00164, -0.00152), (-0.00164, 0.99999, 0.00308), (0.00152, -0.00308, 0.99999)246.33563, 246.17461, 148.84818
2generate(0.99947, 0.0061, 0.03203), (0.00417, -0.99821, 0.05974), (0.03234, -0.05957, -0.9977)196.54251, 98.19156, 97.63085
3generate(0.99939, 0.00797, 0.03387), (0.00587, -0.99809, 0.06156), (0.03429, -0.06133, -0.99753)148.16568, 49.88283, 50.02044
4generate(-0.02277, 0.04661, 0.99865), (0.99974, 0.0027, 0.02267), (-0.00164, 0.99891, -0.04666)97.34286, 194.04362, 97.87107
5generate(0.99943, -0.00324, 0.03367), (0.00415, 0.99963, -0.02696), (-0.03357, 0.02709, 0.99907)48.01399, 146.20187, 50.69334
6generate(-0.99959, -0.01915, -0.02113), (0.02168, -0.02904, -0.99934), (0.01852, -0.99939, 0.02944)147.27696, 147.75333, 50.34828
7generate(-0.9996, -0.01929, -0.02056), (0.02109, -0.02788, -0.99939), (0.0187, -0.99943, 0.02827)195.72841, 196.02829, 97.88367
8generate(0.00518, -0.99994, 0.00977), (0.99983, 0.00501, -0.01756), (0.01751, 0.00986, 0.9998)196.87617, 292.03571, 196.43922
9generate(0.0023, -0.99994, 0.01082), (0.99989, 0.00215, -0.01446), (0.01444, 0.01085, 0.99984)148.49939, 243.81952, 148.83624
10generate(0.00428, 0.99994, -0.0099), (0.99983, -0.00445, -0.01793), (-0.01797, -0.00982, -0.99979)50.46099, 47.50018, 49.98738
11generate(0.99957, 0.02148, 0.02002), (-0.01978, -0.01131, 0.99974), (0.02171, -0.99971, -0.01088)98.32037, 96.62315, 97.8279
12generate(-0.00078, 0.99993, -0.01155), (-0.99988, -0.00096, -0.01541), (-0.01542, 0.01154, 0.99981)248.65833, 148.35861, 148.89571
13generate(-0.0027, 0.99992, -0.01195), (-0.9999, -0.00287, -0.01401), (-0.01404, 0.01191, 0.99983)297.13226, 196.70517, 196.35144
14generate(0.01676, -0.04606, -0.9988), (0.99984, 0.00745, 0.01643), (0.00668, -0.99891, 0.04618)150.05875, 145.57765, 148.48975
15generate(-0.02028, 0.04604, 0.99873), (0.99979, -0.00199, 0.0204), (0.00293, 0.99894, -0.04599)199.11589, 193.77959, 196.05844
DetailsTHE BIOMOLECULE CONSISTS OF A MOLECULEFORMED BY SPACEGROUP SYMMETRY EXPANSION OF THEASYMMETRIC UNIT. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRICUNIT OF THE PROTEIN ASSEMBLY.

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE / TYPE II DEHYDROQUINASE


Mass: 16700.801 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: RATIONALLY DESIGNED BIFUNCTIONAL INHIBITOR / Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PDHQ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 1763 molecules

#2: Chemical
ChemComp-CA2 / (1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID / 1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)-CYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 310.342 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H22O6
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1731 / 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: 2.4 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.5
Details: 15% PEG8K, 0.2M NAKPHOSPHATE, 0.1M MOPS/HCL PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 25, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 3557702 / % possible obs: 93.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 2.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GU1
Resolution: 1.7→27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.669 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SUPERLATTICE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.248 123052 5 %RANDOM
Rwork0.197 ---
obs0.199 2328347 75.8 %-
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: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0.05 Å2-0.21 Å2
2---0.89 Å20.31 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13452 0 388 1731 15571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021227205
X-RAY DIFFRACTIONr_bond_other_d0.0030.02203386
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.94309283
X-RAY DIFFRACTIONr_angle_other_deg1.6793470901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.688528426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99423.9110765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7591532898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.436151550
X-RAY DIFFRACTIONr_chiral_restr0.1140.234759
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02256607
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0245179
X-RAY DIFFRACTIONr_nbd_refined0.2250.26660
X-RAY DIFFRACTIONr_nbd_other0.2090.228446
X-RAY DIFFRACTIONr_nbtor_refined0.1880.214551
X-RAY DIFFRACTIONr_nbtor_other0.0940.216419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.25572
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3410.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.2104
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2381.5178073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4952226612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.489393572
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3984.582664
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A10450tight positional0.090.05
2B10450tight positional0.070.05
3C10450tight positional0.090.05
4D10450tight positional0.090.05
5E10450tight positional0.080.05
6F10450tight positional0.080.05
7G10450tight positional0.080.05
8H10450tight positional0.070.05
9I10450tight positional0.080.05
10J10450tight positional0.080.05
11K10450tight positional0.10.05
12L10450tight positional0.080.05
1A15801medium positional0.20.5
2B15801medium positional0.190.5
3C15801medium positional0.220.5
4D15801medium positional0.220.5
5E15801medium positional0.220.5
6F15801medium positional0.210.5
7G15801medium positional0.240.5
8H15801medium positional0.190.5
9I15801medium positional0.190.5
10J15801medium positional0.20.5
11K15801medium positional0.210.5
12L15801medium positional0.20.5
1A10450tight thermal0.30.5
2B10450tight thermal0.270.5
3C10450tight thermal0.280.5
4D10450tight thermal0.290.5
5E10450tight thermal0.310.5
6F10450tight thermal0.290.5
7G10450tight thermal0.310.5
8H10450tight thermal0.280.5
9I10450tight thermal0.280.5
10J10450tight thermal0.280.5
11K10450tight thermal0.310.5
12L10450tight thermal0.270.5
1A15801medium thermal0.832
2B15801medium thermal0.792
3C15801medium thermal0.832
4D15801medium thermal0.832
5E15801medium thermal0.842
6F15801medium thermal0.792
7G15801medium thermal0.862
8H15801medium thermal0.812
9I15801medium thermal0.812
10J15801medium thermal0.832
11K15801medium thermal0.852
12L15801medium thermal0.832
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.348 10488
Rwork0.275 199751
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.09030.0042-0.00640.0883-0.01230.066-0.0041-0.0028-0.01080.0014-0.00020.0030.0037-0.00470.0043-0.0109-0.0066-0.004-0.0261-0.0099-0.02750.48030.0264-0.3705
20.0753-0.0083-0.00720.10030.00020.0657-0.0003-0.0020.00810.0045-0.00060.00110.00510.00470.001-0.0059-0.00550.0013-0.0001-0.0052-0.0189246.9773246.3505148.5702
30.1415-0.0004-0.01190.0841-0.00940.0730.00690.00180.00530.0079-0.0013-0.0008-0.0025-0.0028-0.0056-0.00660.0060.0003-0.01470.0011-0.028197.087598.276698.0272
40.09310.0075-0.00740.084-0.01840.07550.0004-0.0054-0.0018-0.001-0.0009-0.00260.0016-0.00380.0005-0.00490.0020-0.012-0.0032-0.0184148.691849.92750.3717
50.07420.0057-0.00560.0670.0130.03470.0031-0.00380.00030.0143-0.0024-0.008-0.0040.0072-0.0008-0.00960.0015-0.0064-0.02-0.0042-0.041297.0551194.719597.9131
60.11020.00270.00040.07450.00070.0644-0.00130.0014-0.00190.00550.0016-0.00350.002-0.0021-0.0003-0.0134-0.0011-0.0037-0.0207-0.0093-0.029848.5508146.313250.3443
70.1052-0.0025-0.00640.0563-0.00770.0574-0.00550.0125-0.0006-0.0083-0.0004-0.002-0.00110.00090.0059-0.0198-0.0047-0.0051-0.032-0.0039-0.0388146.8271148.209550.3457
80.1242-0.00350.00540.0778-0.01860.0673-0.0007-0.00050.001-0.00460.00220.0040.0038-0.002-0.0015-0.00730.0006-0.0003-0.014-0.0003-0.0283195.3115196.529197.9162
90.09710.0085-0.01820.08970.00440.0921-0.00170.0129-0.0013-0.00590.0017-0.00480.00210.00510.0001-0.00650.003-0.0036-0.0096-0.0058-0.0171196.9942292.7731196.2014
100.11730.0036-0.00730.09740.00670.0899-0.00430.0080.0081-0.00010.00430.0061-0.0080.00470-0.00690.00370.0018-0.01590.0018-0.0263148.5957244.5363148.554
110.0882-0.01930.00720.0794-0.00710.067500.00470.00270-0.00050.00070.0003-0.0040.0004-0.0112-0.0065-0.0024-0.0226-0.0046-0.038450.476248.089250.3179
120.1080.0048-0.02260.084-0.01840.0827-0.0043-0.00430.00160.0010.0005-0.00040.0007-0.00570.00380.0002-0.0077-0.00020.006-0.0078-0.020598.842696.422397.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 2350
2X-RAY DIFFRACTION2B2 - 2350
3X-RAY DIFFRACTION3C2 - 2350
4X-RAY DIFFRACTION4D2 - 2350
5X-RAY DIFFRACTION5E2 - 2350
6X-RAY DIFFRACTION6F2 - 2350
7X-RAY DIFFRACTION7G2 - 2350
8X-RAY DIFFRACTION8H2 - 2350
9X-RAY DIFFRACTION9I2 - 2350
10X-RAY DIFFRACTION10J2 - 2350
11X-RAY DIFFRACTION11K2 - 2350
12X-RAY DIFFRACTION12L2 - 2350

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