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- PDB-6cv6: Crystal structure of 3-dehydroquinate dehydratase, type II, from ... -

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Basic information

Entry
Database: PDB / ID: 6cv6
TitleCrystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815
Components3-dehydroquinate dehydratase
KeywordsLYASE / SSGCID / chorismate biosynthesis / 3-dehydroshikimate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


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 / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)225,86549
Polymers220,42712
Non-polymers5,43937
Water11,422634
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,49313
Polymers55,1073
Non-polymers1,38610
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,45712
Polymers55,1073
Non-polymers1,3519
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,45712
Polymers55,1073
Non-polymers1,3519
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,45712
Polymers55,1073
Non-polymers1,3519
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.390, 152.390, 177.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-203-

TAR

21B-204-

CL

31K-202-

TAR

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 or (resid 2 through 3...
21(chain B and (resid 1 or (resid 2 through 3...
31(chain C and (resid 1 or (resid 2 through 3...
41(chain D and (resid 1 through 16 or (resid 17...
51(chain E and (resid 1 or (resid 2 through 3...
61(chain F and (resid 1 or (resid 2 through 3...
71(chain G and (resid 1 or (resid 2 through 3...
81(chain H and (resid 1 through 2 or (resid 3...
91(chain I and (resid 1 or (resid 2 through 3...
101(chain J and (resid 1 through 21 or (resid 22...
111(chain K and (resid 1 through 144 or resid 200))
121(chain L and (resid 1 through 16 or (resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 or (resid 2 through 3...A1
121(chain A and (resid 1 or (resid 2 through 3...A2 - 3
131(chain A and (resid 1 or (resid 2 through 3...A1 - 201
141(chain A and (resid 1 or (resid 2 through 3...A1 - 201
151(chain A and (resid 1 or (resid 2 through 3...A1 - 201
161(chain A and (resid 1 or (resid 2 through 3...A1 - 201
211(chain B and (resid 1 or (resid 2 through 3...B1
221(chain B and (resid 1 or (resid 2 through 3...B2 - 3
231(chain B and (resid 1 or (resid 2 through 3...B0 - 201
241(chain B and (resid 1 or (resid 2 through 3...B0 - 201
251(chain B and (resid 1 or (resid 2 through 3...B0 - 201
261(chain B and (resid 1 or (resid 2 through 3...B0 - 201
311(chain C and (resid 1 or (resid 2 through 3...C1
321(chain C and (resid 1 or (resid 2 through 3...C2 - 3
331(chain C and (resid 1 or (resid 2 through 3...C0 - 200
341(chain C and (resid 1 or (resid 2 through 3...C0 - 200
351(chain C and (resid 1 or (resid 2 through 3...C0 - 200
361(chain C and (resid 1 or (resid 2 through 3...C0 - 200
411(chain D and (resid 1 through 16 or (resid 17...D1 - 16
421(chain D and (resid 1 through 16 or (resid 17...D17
431(chain D and (resid 1 through 16 or (resid 17...D1 - 200
441(chain D and (resid 1 through 16 or (resid 17...D1 - 200
451(chain D and (resid 1 through 16 or (resid 17...D1 - 200
461(chain D and (resid 1 through 16 or (resid 17...D1 - 200
511(chain E and (resid 1 or (resid 2 through 3...E1
521(chain E and (resid 1 or (resid 2 through 3...E2 - 3
531(chain E and (resid 1 or (resid 2 through 3...E0 - 201
541(chain E and (resid 1 or (resid 2 through 3...E0 - 201
551(chain E and (resid 1 or (resid 2 through 3...E0 - 201
561(chain E and (resid 1 or (resid 2 through 3...E0 - 201
611(chain F and (resid 1 or (resid 2 through 3...F1
621(chain F and (resid 1 or (resid 2 through 3...F2 - 3
631(chain F and (resid 1 or (resid 2 through 3...F1 - 201
641(chain F and (resid 1 or (resid 2 through 3...F1 - 201
651(chain F and (resid 1 or (resid 2 through 3...F1 - 201
661(chain F and (resid 1 or (resid 2 through 3...F1 - 201
711(chain G and (resid 1 or (resid 2 through 3...G1
721(chain G and (resid 1 or (resid 2 through 3...G2 - 3
731(chain G and (resid 1 or (resid 2 through 3...G1 - 201
741(chain G and (resid 1 or (resid 2 through 3...G1 - 201
751(chain G and (resid 1 or (resid 2 through 3...G1 - 201
761(chain G and (resid 1 or (resid 2 through 3...G1 - 201
811(chain H and (resid 1 through 2 or (resid 3...H1 - 2
821(chain H and (resid 1 through 2 or (resid 3...H3
831(chain H and (resid 1 through 2 or (resid 3...H1 - 201
841(chain H and (resid 1 through 2 or (resid 3...H1 - 201
851(chain H and (resid 1 through 2 or (resid 3...H1 - 201
861(chain H and (resid 1 through 2 or (resid 3...H1 - 201
911(chain I and (resid 1 or (resid 2 through 3...I1
921(chain I and (resid 1 or (resid 2 through 3...I2 - 3
931(chain I and (resid 1 or (resid 2 through 3...I0 - 201
941(chain I and (resid 1 or (resid 2 through 3...I0 - 201
951(chain I and (resid 1 or (resid 2 through 3...I0 - 201
961(chain I and (resid 1 or (resid 2 through 3...I0 - 201
1011(chain J and (resid 1 through 21 or (resid 22...J1 - 21
1021(chain J and (resid 1 through 21 or (resid 22...J22 - 23
1031(chain J and (resid 1 through 21 or (resid 22...J1 - 201
1041(chain J and (resid 1 through 21 or (resid 22...J1 - 201
1051(chain J and (resid 1 through 21 or (resid 22...J1 - 201
1061(chain J and (resid 1 through 21 or (resid 22...J1 - 201
1111(chain K and (resid 1 through 144 or resid 200))K0
1211(chain L and (resid 1 through 16 or (resid 17...L1 - 16
1221(chain L and (resid 1 through 16 or (resid 17...L17
1231(chain L and (resid 1 through 16 or (resid 17...L1 - 201

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Components

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


Mass: 18368.883 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (bacteria) / Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: aroQ, Bphy_6025 / Plasmid: BuphA.00086.c.A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B2JVW0, 3-dehydroquinate dehydratase
#2: Chemical...
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Qiagen JCSG Core screen 1: 20% PEG 3350, 200mM Sodium tartrate; BuphA.00086.c.A1.PS01351 at 20.45mg/ml: cryo: 20% EG: tray 230470b7: puck HXC6-14

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.033171 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033171 Å / Relative weight: 1
ReflectionResolution: 2.6→46.515 Å / Num. obs: 64793 / % possible obs: 99.8 % / Redundancy: 7.326 % / Biso Wilson estimate: 31.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.123 / Χ2: 0.935 / Net I/σ(I): 17.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.3450.5364.0147360.8850.576100
2.67-2.747.3990.4664.6145850.9220.5100
2.74-2.827.4230.4025.3145140.9380.431100
2.82-2.917.4420.3376.3743340.9550.362100
2.91-37.4370.2747.7842440.970.294100
3-3.117.4270.239.0140930.9790.246100
3.11-3.237.4290.16812.2139550.9880.181100
3.23-3.367.410.1461438250.990.156100
3.36-3.517.3750.11517.0636520.9940.124100
3.51-3.687.3750.09720.3135280.9970.10499.9
3.68-3.887.340.08123.8833510.9970.08799.9
3.88-4.117.3230.06827.5631740.9980.07399.9
4.11-4.47.2850.06428.729870.9980.06999.8
4.4-4.757.2490.06329.4227900.9980.06899.6
4.75-5.27.1750.05930.6925810.9980.06499.6
5.2-5.817.0710.06926.7923500.9970.07599.5
5.81-6.717.1240.07325.1520800.9970.07999.1
6.71-8.227.1710.04735.9117820.9990.05199.2
8.22-11.636.9150.02952.7814190.9990.03198.7
11.63-46.5156.3940.02852.378130.9990.0393.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3063)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uqr, selected by Morda

1uqr


Resolution: 2.6→46.515 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.41
RfactorNum. reflection% reflection
Rfree0.2009 2070 3.2 %
Rwork0.1556 --
obs0.157 64747 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.39 Å2 / Biso mean: 43.335 Å2 / Biso min: 4.8 Å2
Refinement stepCycle: final / Resolution: 2.6→46.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13371 0 361 637 14369
Biso mean--79.92 37.23 -
Num. residues----1737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7292X-RAY DIFFRACTION9.387TORSIONAL
12B7292X-RAY DIFFRACTION9.387TORSIONAL
13C7292X-RAY DIFFRACTION9.387TORSIONAL
14D7292X-RAY DIFFRACTION9.387TORSIONAL
15E7292X-RAY DIFFRACTION9.387TORSIONAL
16F7292X-RAY DIFFRACTION9.387TORSIONAL
17G7292X-RAY DIFFRACTION9.387TORSIONAL
18H7292X-RAY DIFFRACTION9.387TORSIONAL
19I7292X-RAY DIFFRACTION9.387TORSIONAL
110J7292X-RAY DIFFRACTION9.387TORSIONAL
111K7292X-RAY DIFFRACTION9.387TORSIONAL
112L7292X-RAY DIFFRACTION9.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.66060.23621440.188641134257100
2.6606-2.72710.25451270.193341374264100
2.7271-2.80080.29671290.192741094238100
2.8008-2.88320.2571170.183941434260100
2.8832-2.97630.2491440.180541394283100
2.9763-3.08270.26541390.185841304269100
3.0827-3.2060.24181260.172941664292100
3.206-3.35190.21141410.173641274268100
3.3519-3.52860.20131580.157941404298100
3.5286-3.74960.22321390.149341704309100
3.7496-4.03890.17721340.130142094343100
4.0389-4.44510.16281420.123241784320100
4.4451-5.08760.1451430.125442304373100
5.0876-6.40720.16381380.152942574395100
6.4072-46.5220.17031490.15044429457899
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)
11.55860.4157-0.48511.6049-0.04631.59440.0536-0.12230.16930.2882-0.06750.1871-0.1623-0.20350.03920.2392-0.00870.02430.169-0.06170.2136-43.25-14.130523.4002
22.49810.1879-0.22211.70310.42570.69770.0181-0.05330.14770.0177-0.0382-0.0011-0.23720.0980.01220.2296-0.0645-0.03220.12780.02940.1724-21.6758-5.3213.9776
31.0161-0.0072-0.01181.5305-0.11262.01780.08790.2420.0617-0.2836-0.0966-0.0710.03780.1390.00740.24580.08680.01780.21820.03340.132-31.112138.902213.8793
41.1412-0.3343-0.0091.51440.39720.40850.01970.0257-0.1067-0.0572-0.0244-0.10480.410.360.00560.35050.13350.03610.25360.01030.1728-23.47617.239633.2578
51.5276-0.53490.43861.4419-0.13831.8493-0.09750.10610.3509-0.0361-0.00690.2971-0.3913-0.1990.06570.24630.0555-0.06430.1852-0.00620.3409-50.506-6.7965-5.1513
61.83530.4724-0.32071.5863-0.06731.6189-0.02660.1915-0.2975-0.1613-0.1130.19720.3341-0.17080.08310.32510.0033-0.02970.1681-0.08070.2602-51.97518.852223.6255
71.38140.4574-0.30291.8762-0.28511.11670.03330.0577-0.0112-0.14630.0548-0.0529-0.0044-0.042-0.08570.3542-0.1916-0.00840.32230.01460.2110.3799.8461-12.1581
81.43110.3707-0.03470.8248-0.71031.15080.02530.16040.0029-0.29350.0974-0.16380.02310.2562-0.08030.465-0.2080.12620.4337-0.0960.326936.758713.7516-26.4812
91.23470.03480.14551.5655-0.49171.50540.06950.20970.2986-0.14010.16920.1679-0.2468-0.1468-0.22440.566-0.17810.15980.38760.08320.398715.404835.154-28.1452
100.7317-0.32790.2151.0305-0.2430.72170.09360.0768-0.3381-0.14050.07580.04050.43220.061-0.05320.82210.242-0.29890.408-0.15030.6842-58.49519.0374-58.145
110.3165-0.0859-0.05350.2745-0.05280.14440.02560.0107-0.2161-0.0028-0.0101-0.12550.17550.12770.06830.91790.4907-0.32020.6411-0.18760.8125-32.28114.782-43.7104
120.5155-0.2462-0.16321.8041-0.77840.71810.0787-0.087-0.32040.05760.10250.10330.34730.0637-0.1050.87260.1934-0.31480.3534-0.00910.6176-57.432619.8415-28.0859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 201)A1 - 201
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 201)B0 - 201
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 200)C0 - 200
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 200)D1 - 200
5X-RAY DIFFRACTION5(chain 'E' and resid 0 through 201)E0 - 201
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 201)F1 - 201
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 201)G1 - 201
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 201)H1 - 201
9X-RAY DIFFRACTION9(chain 'I' and resid 0 through 201)I0 - 201
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 201)J1 - 201
11X-RAY DIFFRACTION11(chain 'K' and resid 1 through 144)K1 - 144
12X-RAY DIFFRACTION12(chain 'L' and resid 1 through 201)L1 - 201

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