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- PDB-3kip: Crystal structure of type-II 3-dehydroquinase from C. albicans -

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Basic information

Entry
Database: PDB / ID: 3kip
TitleCrystal structure of type-II 3-dehydroquinase from C. albicans
Components3-dehydroquinase, type II
KeywordsLYASE
Function / homology
Function and homology information


quinate metabolic process / 3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity
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
Catabolic 3-dehydroquinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsTrapani, S. / Schoehn, G. / Navaza, J. / Abergel, C.
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.
Authors: Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel /
Abstract: The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing ...The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinase, type II
B: 3-dehydroquinase, type II
C: 3-dehydroquinase, type II
D: 3-dehydroquinase, type II
E: 3-dehydroquinase, type II
F: 3-dehydroquinase, type II
G: 3-dehydroquinase, type II
H: 3-dehydroquinase, type II
I: 3-dehydroquinase, type II
J: 3-dehydroquinase, type II
K: 3-dehydroquinase, type II
L: 3-dehydroquinase, type II
M: 3-dehydroquinase, type II
N: 3-dehydroquinase, type II
O: 3-dehydroquinase, type II
P: 3-dehydroquinase, type II
Q: 3-dehydroquinase, type II
R: 3-dehydroquinase, type II
S: 3-dehydroquinase, type II
T: 3-dehydroquinase, type II
U: 3-dehydroquinase, type II
V: 3-dehydroquinase, type II
W: 3-dehydroquinase, type II
X: 3-dehydroquinase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,62956
Polymers443,34624
Non-polymers3,28332
Water3,027168
1
A: 3-dehydroquinase, type II
B: 3-dehydroquinase, type II
C: 3-dehydroquinase, type II
D: 3-dehydroquinase, type II
E: 3-dehydroquinase, type II
F: 3-dehydroquinase, type II
G: 3-dehydroquinase, type II
H: 3-dehydroquinase, type II
I: 3-dehydroquinase, type II
J: 3-dehydroquinase, type II
K: 3-dehydroquinase, type II
L: 3-dehydroquinase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,31428
Polymers221,67312
Non-polymers1,64116
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28980 Å2
ΔGint-262 kcal/mol
Surface area65450 Å2
MethodPISA
2
M: 3-dehydroquinase, type II
N: 3-dehydroquinase, type II
O: 3-dehydroquinase, type II
P: 3-dehydroquinase, type II
Q: 3-dehydroquinase, type II
R: 3-dehydroquinase, type II
S: 3-dehydroquinase, type II
T: 3-dehydroquinase, type II
U: 3-dehydroquinase, type II
V: 3-dehydroquinase, type II
W: 3-dehydroquinase, type II
X: 3-dehydroquinase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,31428
Polymers221,67312
Non-polymers1,64116
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28810 Å2
ΔGint-261 kcal/mol
Surface area66460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61720 Å2
ΔGint-535 kcal/mol
Surface area127980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.103, 308.110, 97.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a dodecamer. There are 2 biological units in the asymmetric unit (chains A-L and chains M-X).

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Components

#1: Protein ...
3-dehydroquinase, type II


Mass: 18472.744 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: NIH 3147 ATCC number MYA-2876D / Gene: DQD1, DHQ99, CaO19.9823 / Plasmid: pSF-04 Protein'eXpert / Production host: Escherichia coli (E. coli) / References: UniProt: Q59Z17, 3-dehydroquinate dehydratase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 14% PEG 8000 (w/v), LiSO4 0.2 M, Hepes buffer 0.1 M, pH 7.0, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorDate: 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→70.68 Å / Num. all: 101344 / Num. obs: 101228 / % possible obs: 99.89 % / Redundancy: 6.4 % / Biso Wilson estimate: 77.8 Å2 / Rsym value: 0.136 / Net I/σ(I): 4.3
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 14646 / Rsym value: 0.539 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a 3D EM reconstruction at 15 A resolution

Resolution: 2.95→70.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.963 / SU B: 34.706 / SU ML: 0.299 / SU R Cruickshank DPI: 0.339 / SU Rfree: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5090 5 %RANDOM
Rwork0.203 ---
obs0.205 101228 99.89 %-
all-101344 --
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 max: 143.44 Å2 / Biso mean: 59.277 Å2 / Biso min: 12.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.95→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26792 0 184 168 27144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02227378
X-RAY DIFFRACTIONr_angle_refined_deg2.2711.95437140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16953409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24524.4591256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.968154536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.42615144
X-RAY DIFFRACTIONr_chiral_restr0.1520.24358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0220368
X-RAY DIFFRACTIONr_mcbond_it0.941.517050
X-RAY DIFFRACTIONr_mcangle_it1.826227438
X-RAY DIFFRACTIONr_scbond_it2.967310328
X-RAY DIFFRACTIONr_scangle_it4.934.59702
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 372 -
Rwork0.35 7026 -
all-7398 -
obs--100 %
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)
12.4199-0.48670.49733.65620.38844.3025-0.11250.1893-0.1498-0.2964-0.05230.4049-0.1364-0.29320.1648-0.6751-0.0443-0.0394-0.8688-0.0852-0.485143.075100.08414.168
24.4406-0.59460.07323.88960.00071.3580.02390.0868-0.3344-0.05440.0151-0.27270.26430.0438-0.039-0.5905-0.020.0015-0.8596-0.0881-0.497264.46486.16430.266
34.48961.1959-0.41252.5930.95363.75170.0914-0.338-0.33160.376-0.23090.37280.2747-0.25640.1395-0.6069-0.06920.1369-0.8097-0.0615-0.459736.55190.11742.222
43.4911-0.92420.04932.2738-0.27184.4233-0.0058-0.56170.13340.43170.0106-0.2577-0.10010.0743-0.0048-0.5932-0.0298-0.0343-0.725-0.0188-0.594380.962117.06960.733
53.7306-0.1011-0.99614.11821.04032.21470.00830.0247-0.47740.0807-0.0503-0.190.22190.17720.042-0.70480.03-0.0352-0.8812-0.0395-0.544884.3100.73134.859
62.93841.3760.1945.3244-0.75252.3122-0.030.18260.2911-0.07520.0183-0.2922-0.13210.14740.0117-0.71310.02480.0258-0.86230.0049-0.472684.253131.37733.797
73.1835-0.21971.60884.46150.70993.88970.10510.38980.0175-0.5578-0.0610.4226-0.032-0.1878-0.0441-0.60390.0025-0.0823-0.781-0.0001-0.408640.168124.98612.199
81.9151-0.8752-0.82774.95470.35933.7528-0.0551-0.0780.39040.27630.0620.5361-0.345-0.3246-0.0069-0.62720.080.0217-0.8279-0.064-0.362340.589145.00135.674
93.32120.48080.24632.76240.5862.3984-0.04170.2340.2821-0.29250.0012-0.133-0.24820.12310.0405-0.6620.0186-0.0021-0.93040.0557-0.467865.544140.35819.987
104.29470.28090.73882.7491.31944.36860.0405-0.57760.04220.565-0.02680.0262-0.02520.1483-0.0137-0.4472-0.04830.1123-0.623-0.0781-0.646459.093123.09171.657
114.5881-1.0808-0.42084.2189-0.54373.14150.0847-0.27540.35770.3013-0.09390.3283-0.342-0.39520.0092-0.49470.05180.1827-0.6595-0.1408-0.485534.234133.57957.46
122.22091.2989-0.1945.1363-0.46824.125-0.0669-0.2872-0.16480.413-0.03620.3520.3487-0.45620.1031-0.4707-0.05450.2127-0.6322-0.0566-0.523336.955103.94663.523
132.75030.2749-0.67834.4905-0.03773.7379-0.04690.01580.2603-0.11980.1543-0.3511-0.3050.3066-0.1074-0.6443-0.06620.016-0.7911-0.0902-0.452370.7772.923.765
144.008-0.4639-0.45352.5940.95322.59740.0881-0.12830.28650.0215-0.16740.3478-0.2476-0.24680.0793-0.5987-0.05550.047-0.7891-0.0985-0.432843.56670.0216.601
153.48350.17221.36743.4422-0.33483.00150.1867-0.5936-0.12770.4207-0.0418-0.24290.29740.0594-0.1449-0.4658-0.0071-0.0561-0.6934-0.032-0.457267.28153.25427.41
164.0740.8311-0.60033.6877-1.20932.79630.1203-0.1788-0.47780.2029-0.04810.17880.3731-0.3292-0.0722-0.5577-0.0936-0.0248-0.77280.0316-0.459924.99431.709-0.557
173.4446-0.78430.69264.30151.19583.2445-0.0452-0.34610.41190.1472-0.01980.3198-0.1871-0.4040.065-0.7227-0.02670.038-0.8144-0.0691-0.409226.42562.040.016
183.63590.77080.50952.33920.43174.2113-0.03930.47580.0826-0.28140.06760.178-0.01690.0894-0.0282-0.6497-0.00130.0033-0.8037-0.011-0.48832.3847.002-25.879
195.36361.2612-0.50553.87210.80423.27590.08960.25140.2609-0.1020.0294-0.3518-0.26940.5582-0.119-0.6595-0.06010.0923-0.5973-0.0851-0.464378.95460.812-17.009
202.3874-0.897-0.76144.60650.47424.1465-0.04170.2628-0.384-0.03950.11-0.3040.48620.5113-0.0683-0.55670.09620.0274-0.6389-0.1679-0.368575.24231.306-22.785
214.28810.27560.8663.398-1.14534.1273-0.08820.5957-0.0424-0.47860.21-0.0565-0.00890.0326-0.1217-0.6155-0.01330.0643-0.5906-0.0666-0.576855.7951.305-34.124
225.11031.02751.12414.66080.32071.61710.0983-0.125-0.49080.18190.01880.31240.4769-0.2318-0.1171-0.3341-0.0612-0.0589-0.80490.1147-0.351843.07215.5916.289
233.0401-1.1346-0.77472.898-0.7594.17080.18090.1491-0.5983-0.1414-0.0892-0.33540.48260.3526-0.0917-0.43570.1181-0.0643-0.7825-0.0601-0.224972.03217.773-1.468
241.97450.20721.1463.77550.23955.2760.1234-0.3548-0.26410.5205-0.0462-0.38860.10740.2206-0.0772-0.3280.0174-0.1108-0.72770.0685-0.39862.73328.58925.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 200
2X-RAY DIFFRACTION2B1 - 200
3X-RAY DIFFRACTION3C1 - 200
4X-RAY DIFFRACTION4D1 - 200
5X-RAY DIFFRACTION5E1 - 200
6X-RAY DIFFRACTION6F1 - 200
7X-RAY DIFFRACTION7G1 - 200
8X-RAY DIFFRACTION8H1 - 200
9X-RAY DIFFRACTION9I1 - 200
10X-RAY DIFFRACTION10J1 - 200
11X-RAY DIFFRACTION11K1 - 200
12X-RAY DIFFRACTION12L1 - 200
13X-RAY DIFFRACTION13M1 - 200
14X-RAY DIFFRACTION14N1 - 200
15X-RAY DIFFRACTION15O1 - 200
16X-RAY DIFFRACTION16P1 - 200
17X-RAY DIFFRACTION17Q1 - 200
18X-RAY DIFFRACTION18R1 - 200
19X-RAY DIFFRACTION19S1 - 200
20X-RAY DIFFRACTION20T1 - 200
21X-RAY DIFFRACTION21U1 - 200
22X-RAY DIFFRACTION22V1 - 200
23X-RAY DIFFRACTION23W1 - 200
24X-RAY DIFFRACTION24X1 - 200

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