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- PDB-3mwb: The Crystal Structure of Prephenate dehydratase in complex with L... -

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Basic information

Entry
Database: PDB / ID: 3mwb
TitleThe Crystal Structure of Prephenate dehydratase in complex with L-Phe from Arthrobacter aurescens to 2.0A
ComponentsPrephenate dehydratase
KeywordsLYASE / L-Phe / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / chorismate mutase activity / L-phenylalanine biosynthetic process / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #500 / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain / ACT domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #500 / Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain / ACT domain profile. / ACT domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Prephenate dehydratase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsStein, A.J. / Chhor, G. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of Prephenate dehydratase in complex with L-Phe from Arthrobacter aurescens to 2.0A
Authors: Stein, A.J. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8245
Polymers66,4692
Non-polymers3553
Water5,423301
1
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules

A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,64710
Polymers132,9384
Non-polymers7096
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11180 Å2
ΔGint-89 kcal/mol
Surface area46800 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-27 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.120, 107.155, 137.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsBiological unit is the same as asymmetric unit.

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Components

#1: Protein Prephenate dehydratase /


Mass: 33234.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: pheA, AAur_0101 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1R118, prephenate dehydratase
#2: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris pH 8.5, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42250 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.107 / Χ2: 1.936 / Net I/av σ(I): 24.151 / Net I/σ(I): 7.7 / Num. measured all: 252235
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.076.10.61741531.1151100
2.07-2.156.10.4641651.1561100
2.15-2.255.70.4141842.465199.9
2.25-2.375.90.33441931.6071100
2.37-2.526.10.19642071.243199.9
2.52-2.716.10.15441951.361100
2.71-2.996.10.11142251.5541100
2.99-3.4260.08542442.2321100
3.42-4.315.80.07242633.085199.9
4.31-505.70.06444213.643199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
RefinementResolution: 2→42.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.674 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2115 5.1 %RANDOM
Rwork0.21 ---
obs0.212 41788 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 25 301 4768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224647
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.966383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6045629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48823.511188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16515658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5041534
X-RAY DIFFRACTIONr_chiral_restr0.0790.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213607
X-RAY DIFFRACTIONr_mcbond_it0.4711.53085
X-RAY DIFFRACTIONr_mcangle_it0.79624951
X-RAY DIFFRACTIONr_scbond_it1.51631562
X-RAY DIFFRACTIONr_scangle_it2.3064.51420
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 131 -
Rwork0.238 2777 -
all-2908 -
obs--94.32 %
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)
11.68192.1353-1.40153.97760.40434.9887-0.18940.10220.2003-0.2635-0.00960.49060.213-0.35380.19890.1272-0.02-0.05020.2211-0.02030.149927.051121.441238.9021
25.3992-0.2687-2.0230.7868-2.12887.2766-0.06540.4876-0.49-0.37270.34470.25761.0125-1.3328-0.27930.39860.0588-0.24460.4904-0.20080.564720.306625.235236.3532
39.69781.512812.99483.5970.318719.1011-0.1624-0.1397-0.3511-0.19990.16950.09590.0819-0.0202-0.00710.15390.05520.13570.17240.11830.400831.826320.788937.0216
46.51231.4984-2.04398.6877-4.195412.3548-0.05380.2782-0.3238-0.3011-0.1531-0.26150.39260.20880.20690.10640.02690.00280.0855-0.0410.036835.462628.98137.5601
56.05753.4882-0.61426.6940.23020.14460.1389-0.5114-0.03540.4532-0.1310.05790.00590.0487-0.00790.1360.02930.04350.18870.00980.085131.625627.201751.0458
611.1922-0.5658-2.28012.6748-0.67075.2130.2830.5521-0.1133-0.1383-0.20880.0154-0.04450.1762-0.07420.1259-0.0014-0.00180.1097-0.03770.016131.421636.716442.2588
74.41320.9821-0.70283.5606-0.82021.4757-0.09830.069-0.5726-0.0890.04520.2290.2796-0.09310.05310.1409-0.01010.03220.1770.02120.244718.43637.572951.3006
818.989711.427-5.51226.902-3.28131.66140.3398-0.6285-0.37620.2731-0.3534-0.2657-0.04640.25140.01360.2504-0.0128-0.03560.29580.02760.232719.914311.499860.0729
90.6713-0.8763-0.452.021.0090.5059-0.1254-0.1682-0.49110.34890.00240.11090.1805-0.03010.12310.1646-0.01780.0630.33760.23610.690923.2835.919855.7029
104.9682-1.68340.28493.8087-0.2086.6851-0.01630.7859-0.6177-0.7662-0.2148-0.23390.2920.07990.23110.2798-0.0380.05430.2326-0.05790.36520.43695.415244.6768
112.08511.81980.47562.2891-0.38721.1340.2689-0.23030.05540.3996-0.17690.2392-0.1468-0.1577-0.0920.11280.0230.06510.1276-0.05210.195320.458625.487451.0064
121.0473-0.6447-0.67971.3727-0.58922.1754-0.06240.16260.0731-0.0145-0.1089-0.114-0.12770.1020.17130.1127-0.0653-0.02810.11060.01180.130432.657444.415750.0044
1330.1987-10.56432.334724.9314-1.25845.73810.2726-0.7535-0.40091.0694-0.1050.1502-0.3450.1593-0.16760.1103-0.0284-0.02460.1036-0.00960.130635.399348.336862.2921
141.51550.17270.165510.81580.39861.7792-0.08420.0245-0.02620.03270.11880.0193-0.10160.0154-0.03470.068-0.030.00390.095-0.02580.009128.000847.179257.624
158.3014-0.9264-4.998811.4731-3.84811.9855-0.32540.0543-1.0045-0.2197-0.1205-0.98780.20110.84460.44590.18640.03690.03990.1771-0.06660.281141.602935.192258.897
161.0986-1.27640.68592.9327-0.77741.6395-0.01280.2123-0.0337-0.0336-0.03860.03470.01590.05540.05140.0611-0.00770.01030.0977-0.03090.024228.665746.575451.2483
174.16112.44711.60653.90181.19862.43040.02730.1061-0.09470.09040.0518-0.2073-0.00990.2281-0.07920.08140.00260.00930.0753-0.00080.014634.464147.615849.7403
183.47621.0982-0.360816.39582.74252.6310.0881-0.23540.16890.5815-0.31960.80070.0847-0.160.23150.0981-0.00230.02010.14990.01230.067316.436248.24253.6611
197.27528.76151.081712.7897-0.15361.1133-0.12930.3369-0.1055-0.11930.0652-0.2715-0.05570.2550.06410.0940.04110.01670.11610.03120.038724.731965.299351.5503
2051.554420.2748-23.057228.1282-26.512525.42360.68252.51612.3075-1.1411-0.9002-0.47490.85480.62970.21760.5232-0.23240.03070.820.27010.248732.187975.739148.9202
212.3812-1.1062-3.14215.0777-0.86115.8822-0.2206-0.2245-0.15380.3278-0.0536-0.31880.20850.18890.27420.16060.0053-0.03060.18480.01750.109541.287610.719767.0815
2217.82748.6746-8.539756.3596-13.91095.9207-0.3022-0.8077-1.56141.0869-0.3759-0.5972-0.11380.42490.67810.36840.0424-0.14720.64280.16540.493948.297913.409573.1037
237.48792.2497-0.06225.7877-0.13736.2877-0.03890.0406-0.08750.2142-0.08910.21360.5462-0.16960.1280.2628-0.03320.03460.1501-0.02630.170635.21089.976369.6349
2423.92583.93253.74214.69031.041517.48090.2012-0.1268-1.06060.23380.14940.92421.0635-1.109-0.35050.3958-0.08670.07210.23290.03730.230130.228811.284576.5014
252.18622.1976-1.94.5993-0.10093.0226-0.0318-0.1037-0.0544-0.0818-0.07790.0111-0.02810.10860.10970.1510.0045-0.01970.1695-0.0260.168836.548520.790862.8824
266.18374.744713.29723.644710.197428.6036-0.338-1.35490.5555-0.2975-0.91160.4716-0.9625-2.98591.24960.39250.39510.1460.8490.10450.925926.701123.487272.4921
272.692-4.0793-4.88346.18487.40578.8713-0.3443-0.0301-0.17530.49910.04950.24910.57430.0760.29480.24240.02490.01730.168-0.0310.147745.625717.210563.5373
285.2884-3.2881-0.83463.69011.05641.83110.20090.4044-0.0425-0.2237-0.16210.0082-0.047-0.0673-0.03880.1277-0.0181-0.00710.12170.02570.104447.21488.84444.4642
299.2365-2.2447-5.78357.73591.898216.8116-0.13690.26750.3791-0.39790.0879-0.14610.0402-0.18830.0490.13230.01620.04030.14320.0840.094250.995516.827341.2326
305.2423-0.5736-1.25853.41811.75054.56260.05580.0697-0.48280.07810.04850.20280.5242-0.3136-0.10430.1683-0.0120.01870.1496-0.00280.136542.80435.346849.4613
3119.07126.87296.389511.4434-2.16584.3678-0.025-0.58530.54760.7683-0.14050.2431-0.3935-0.23490.16540.31560.03770.07710.22350.0460.106350.20681.689658.5881
321.535-1.7495-2.06882.3951.94113.47830.0179-0.10680.16660.0880.107-0.1467-0.16840.1441-0.12490.0866-0.0003-0.04620.1638-0.01470.135846.119718.497663.2791
334.8909-1.3062.36533.6783-0.76523.6215-0.0697-0.4157-0.2930.08050.15130.16660.0786-0.2391-0.08160.1203-0.00390.04190.08490.00060.041232.664536.287673.3137
3424.4345-1.655119.93575.43740.899117.2163-0.00130.49730.3494-0.8502-0.2465-0.1136-0.37530.31850.24790.20990.0030.08590.131-0.06690.151829.119745.611168.9236
350.4812-1.234-0.30625.79754.38325.1233-0.0910.0041-0.0470.24020.0350.12650.09630.09190.05610.07890.02650.00610.08240.02430.110137.295641.221471.8408
3621.61471.02981.55314.1269-4.541715.4169-0.0460.3088-1.2285-0.0380.23130.5420.6384-0.7952-0.18530.1454-0.0567-0.0050.0831-0.01290.204624.876433.926963.7433
371.2437-0.09820.97951.4070.5571.4193-0.08-0.1254-0.16960.11230.0470.01610.04240.05980.0330.10390.05310.01810.09790.06080.112735.196838.663478.8379
3814.7765-7.4613-2.18935.76932.04911.281-0.07030.464-0.21430.1265-0.0390.22250.2495-0.05260.10930.14390.0171-0.00050.1127-0.00010.016234.513831.755575.5447
391.589-3.6126-1.887713.21957.91015.68660.1910.00320.0118-0.49180.1474-0.4836-0.12090.3244-0.33840.07780.0469-0.03660.1829-0.01930.123546.479943.580380.9969
4012.7218-0.8757-10.25072.67371.595919.0953-0.0146-0.6382-0.32910.68830.14980.0760.1672-0.0781-0.13510.19510.0524-0.00690.17230.01080.069535.888753.632895.4764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 16
2X-RAY DIFFRACTION2A17 - 30
3X-RAY DIFFRACTION3A31 - 36
4X-RAY DIFFRACTION4A37 - 54
5X-RAY DIFFRACTION5A55 - 72
6X-RAY DIFFRACTION6A73 - 83
7X-RAY DIFFRACTION7A84 - 109
8X-RAY DIFFRACTION8A110 - 120
9X-RAY DIFFRACTION9A121 - 138
10X-RAY DIFFRACTION10A139 - 169
11X-RAY DIFFRACTION11A170 - 185
12X-RAY DIFFRACTION12A186 - 212
13X-RAY DIFFRACTION13A213 - 218
14X-RAY DIFFRACTION14A219 - 230
15X-RAY DIFFRACTION15A231 - 242
16X-RAY DIFFRACTION16A243 - 258
17X-RAY DIFFRACTION17A259 - 279
18X-RAY DIFFRACTION18A280 - 290
19X-RAY DIFFRACTION19A291 - 303
20X-RAY DIFFRACTION20A304 - 309
21X-RAY DIFFRACTION21B4 - 20
22X-RAY DIFFRACTION22B21 - 26
23X-RAY DIFFRACTION23B27 - 42
24X-RAY DIFFRACTION24B43 - 50
25X-RAY DIFFRACTION25B51 - 69
26X-RAY DIFFRACTION26B70 - 77
27X-RAY DIFFRACTION27B78 - 94
28X-RAY DIFFRACTION28B95 - 113
29X-RAY DIFFRACTION29B114 - 126
30X-RAY DIFFRACTION30B127 - 156
31X-RAY DIFFRACTION31B157 - 163
32X-RAY DIFFRACTION32B164 - 191
33X-RAY DIFFRACTION33B192 - 210
34X-RAY DIFFRACTION34B211 - 218
35X-RAY DIFFRACTION35B219 - 230
36X-RAY DIFFRACTION36B231 - 244
37X-RAY DIFFRACTION37B245 - 266
38X-RAY DIFFRACTION38B267 - 281
39X-RAY DIFFRACTION39B282 - 297
40X-RAY DIFFRACTION40B298 - 309

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