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- PDB-2cjf: TYPE II DEHYDROQUINASE INHIBITOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2cjf
TitleTYPE II DEHYDROQUINASE INHIBITOR COMPLEX
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / DEHYDROQUINASE / SHIKIMATE PATHWAY / DEHYDROQUINATE / DRUG DESIGN / 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
PHOSPHATE ION / Chem-RP4 / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPayne, R.J. / Riboldi-Tunnicliffe, A. / Abell, A.D. / Lapthorn, A.J. / Abell, C.
CitationJournal: Chemmedchem / Year: 2007
Title: Design, synthesis, and structural studies on potent biaryl inhibitors of type II dehydroquinases.
Authors: Payne, R.J. / Riboldi-Tunnicliffe, A. / Kerbarh, O. / Abell, A.D. / Lapthorn, A.J. / Abell, C.
History
DepositionMar 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)206,68444
Polymers200,41012
Non-polymers6,27432
Water28,1211561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)195.755, 195.730, 239.680
Angle α, β, γ (deg.)65.84, 65.89, 89.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00131, 0.99966, 0.02589), (0.99994, -0.0016, 0.01107), (0.0111, 0.02587, -0.9996)194.76367, 97.11488, -0.29481
2given(-0.99974, 0.00086, -0.02261), (0.0009, 1, -0.00182), (0.02261, -0.00184, -0.99974)392.3627, -99.73705, 93.30791
3given(-0.99983, -0.00037, 0.01862), (0.00038, -1, 0.00058), (0.01862, 0.00059, 0.99983)292.45334, 98.73705, -1.82442
4given(0.001, -0.99994, 0.01052), (0.99908, 0.00055, -0.04278), (0.04277, 0.01055, 0.99903)292.3118, -92.27222, -106.9065
5given(-0.0021, -0.99963, 0.02729), (-0.99995, 0.00183, -0.00997), (0.00992, -0.02731, -0.99958)293.69275, 193.57146, 1.50978
6given(-0.00134, -0.99988, -0.01545), (-0.99996, 0.0012, 0.00857), (-0.00855, 0.01547, -0.99984)394.95261, 194.54628, 95.04523
7given(1, 0.0006, 0.00106), (0.0006, -1, -0.00015), (0.00106, 0.00015, -1)97.86295, 198.68971, 97.35522
DetailsTHE BIOMOLECULE CONSISTS OF A MOLECULE FORMED BY SPACEGROUP SYMMETRY EXPANSION OF THE ASYMMETRIC 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): B834(DE3) / Variant (production host): PLYSS / References: UniProt: P15474, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 1593 molecules

#2: Chemical
ChemComp-RP4 / (1S,4S,5S)-1,4,5-TRIHYDROXY-3-[3-(PHENYLTHIO)PHENYL]CYCLOHEX-2-ENE-1-CARBOXYLIC ACID


Mass: 358.408 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C19H18O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1561 / 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

Crystal growMethod: vapor diffusion, sitting drop
Details: PROTEIN AT 6MG/ML WAS EQUILIBRATED AGAINST A SOLUTION 15% PEG 8K, 0.1M HEPES BUFFER PH 7.5 USING THE SITING DROP METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.939283
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939283 Å / Relative weight: 1
ReflectionResolution: 2.2→65 Å / Num. obs: 1334888 / % possible obs: 90.6 % / Redundancy: 1.88 % / Biso Wilson estimate: 25.21 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.3 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BT4

2bt4


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.827 / SU B: 6.641 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE G CHAIN ELECTRON DENSITY IS OF SIGNIFICANTLY POORER QUALITY WHICH IN PART EXPLAINS THE HIGH R -FACTOR AND THE PRESENCE OF ONLY 8 DODECAMERS IN THE ASU AS APPOSED TO 16 IN THE MORE ORDERED 2BT4
RfactorNum. reflection% reflectionSelection details
Rfree0.334 80795 5 %RANDOM
Rwork0.274 ---
obs0.277 1532275 76.2 %-
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: 31.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.59 Å2-0.21 Å2
2---0.36 Å2-0.63 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13452 0 424 1561 15437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021113891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.944155205
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.145514208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6823.9085384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7951516440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77115776
X-RAY DIFFRACTIONr_chiral_restr0.1230.217280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0288552
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.261261
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.261830
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2990.211928
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.2216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.572325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.552113288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.341346092
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3014.541917
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
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.393 2402
Rwork0.359 45138

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