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- PDB-1gu0: CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COE... -

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Basic information

Entry
Database: PDB / ID: 1gu0
TitleCRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / TYPE II DEHYDROQUINASE / SHIKIMATE PATHWAY / DODECAMERIC QUATERNARY STRUCTURE / TETRAHEDRAL SYMMETRY
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
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoszak, A.W. / Krell, T. / Robinson, D. / Hunter, I.S. / Coggins, J.R. / Lapthorn, A.J.
CitationJournal: Structure / Year: 2002
Title: The Structure and Mechanism of the Type II Dehydroquinase from Streptomyces Coelicolor
Authors: Roszak, A.W. / Robinson, D. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionJan 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)199,32416
Polymers198,83512
Non-polymers4894
Water31,3461740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.200, 138.400, 141.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71H
81I
91J
101K
111L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 2 - 150 / Label seq-ID: 2 - 150

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7HH
8II
9JJ
10KK
11LL

NCS oper:
IDCodeMatrixVector
1given(0.00708, 0.92154, -0.38822), (-0.39202, -0.3546, -0.84887), (-0.91993, 0.1582, 0.35875)8.23507, 85.55029, 40.90844
2given(0.00824, -0.39764, -0.9175), (0.91359, -0.37005, 0.16859), (0.40656, -0.83961, 0.36023)71.29705, 17.09995, 61.55885
3given(-0.99996, 0.00502, -0.00776), (0.00909, 0.6851, -0.72839), (0.00166, -0.72843, -0.68512)54.49592, 34.82314, 81.04834
4given(0.00352, 0.91859, -0.3952), (0.38144, 0.36409, 0.84967), (0.92439, -0.15373, -0.3491)8.57029, -16.58185, 24.99649
5given(-0.01303, 0.39936, 0.9167), (-0.91922, -0.36559, 0.1462), (0.39352, -0.84075, 0.37186)-16.52143, 67.34712, 39.30995
6given(-0.00983, -0.91991, 0.39201), (0.39635, -0.3635, -0.84307), (0.91805, 0.14709, 0.36818)46.49717, 64.1228, -9.06398
7given(0.00707, -0.39838, -0.91719), (-0.91702, 0.36319, -0.16482), (0.39878, 0.84225, -0.36276)71.15918, 52.28157, 5.18036
8given(-0.9999, -0.00746, -0.01185), (-0.00348, -0.68764, 0.72605), (-0.01356, 0.72602, 0.68754)54.99685, 34.6108, -14.26512
9given(-0.01603, 0.39654, 0.91788), (0.91913, 0.36724, -0.14261), (-0.39363, 0.84136, -0.37035)-16.17982, 1.6171, 27.03639
10given(0.99974, 0.00264, 0.02249), (0.00281, -0.99997, -0.00725), (0.02247, 0.00731, -0.99972)-0.76468, 69.52921, 65.31114
11given(-0.00256, -0.92118, 0.38913), (0.41263, 0.35543, 0.83869), (0.91089, -0.15842, -0.38102)46.60988, 5.75645, 76.06654

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Components

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


Mass: 16569.605 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PDHQ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1740 / 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: 2.8 Å3/Da / Density % sol: 56.3 %
Crystal growpH: 8.5
Details: PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→75 Å / Num. obs: 429534 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.8→1.82 Å / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DHQ

2dhq


Resolution: 2→24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.428 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 12147 10 %RANDOM
Rwork0.2 ---
obs0.204 6768 66.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13327 0 32 1740 15099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02113631
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212259
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0561.92518585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.953328290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.22117
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215736
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022736
X-RAY DIFFRACTIONr_nbd_refined0.2360.33238
X-RAY DIFFRACTIONr_nbd_other0.2230.312353
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.51427
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1570.513
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.380.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.322
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.544
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1781.58848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.921214091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41134783
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5494.54494
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 738
Rwork0.277 6768
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)
10.10510.02340.03211.0431-0.36170.65460.0169-0.00430.0053-0.0404-0.0473-0.1243-0.1880.04010.03040.1229-0.01260.04010.27760.05680.321936.58559.21313.924
20.54750.31960.73591.5935-0.10310.45480.00430.112-0.0579-0.2974-0.0108-0.2260.04410.13260.00650.12650.0080.09410.31950.02840.306435.33631.1721.659
30.3805-0.2967-0.02150.84370.03921.04270.004-0.01350.00020.0062-0.0924-0.3024-0.03510.31760.08840.0041-0.01990.03210.41910.1250.489457.56638.19421.788
40.56670.1273-0.38720.2193-0.42621.02510.05820.04750.13140.0940.02190-0.2593-0.0274-0.08020.18480.03340.02160.25920.02740.317318.02665.49428.343
50.04910.11710.25810.3290.26980.19920.04-0.04140.03450.1609-0.04180.0098-0.059-0.03080.00180.2456-0.0116-0.00740.267-0.02150.285718.7855.01157.194
60.5260.13060.0440.8535-0.00450.58380.0427-0.04260.03380.019-0.04620.1752-0.0958-0.11910.00350.07160.0330.0190.2951-0.01230.3314-3.21545.49838.043
70.0644-0.1598-0.46380.69830.31691.07330.03990.05280.0133-0.1143-0.05170.030.0139-0.00780.01180.08220.01580.0080.2811-0.00590.270519.25714.2778.703
80.4246-0.4863-0.21810.9799-0.05330.86430.00230.0204-0.0317-0.01420.00970.1709-0.0148-0.1927-0.0120.00370.0104-0.00190.3137-0.00780.3255-3.12723.65527.395
90.2259-0.1421-0.0050.4906-0.28860.8437-0.0135-0.0239-0.0426-0.0075-0.0217-0.02360.1077-0.01590.03520.0458-0.01760.00770.25750.01010.269717.9473.67337.462
100.53610.1384-0.07680.6348-0.39650.9525-0.0592-0.05840.0710.0558-0.0669-0.3527-0.0690.34130.1260.0552-0.0285-0.05880.43890.1060.495957.26631.03345.059
110.07580.0268-0.00810.8864-0.20840.6823-0.05570.00250.0470.0721-0.0133-0.1140.04750.0850.0690.0810.0201-0.02830.28560.0550.289836.15110.01852.274
120.3924-0.3804-0.19531.8874-0.13290.3744-0.0462-0.07340.10720.40870-0.2046-0.06530.12040.04620.2473-0.0061-0.09580.3023-0.00060.306234.56238.0764.602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 150
2X-RAY DIFFRACTION2B2 - 150
3X-RAY DIFFRACTION3C2 - 150
4X-RAY DIFFRACTION4D2 - 150
5X-RAY DIFFRACTION5E2 - 150
6X-RAY DIFFRACTION6F2 - 150
7X-RAY DIFFRACTION7G2 - 150
8X-RAY DIFFRACTION8H2 - 150
9X-RAY DIFFRACTION9I2 - 150
10X-RAY DIFFRACTION10J2 - 150
11X-RAY DIFFRACTION11K2 - 150
12X-RAY DIFFRACTION12L2 - 150

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