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- PDB-3s52: Crystal structure of a putative fumarylacetoacetate hydrolase fam... -

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Basic information

Entry
Database: PDB / ID: 3s52
TitleCrystal structure of a putative fumarylacetoacetate hydrolase family protein from Yersinia pestis CO92
ComponentsPutative fumarylacetoacetate hydrolase family protein
KeywordsHYDROLASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyFumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / isomerase activity / Alpha-Beta Complex / Alpha Beta / Putative isomerase
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.012 Å
AuthorsNocek, B. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative fumarylacetoacetate hydrolase family protein from Yersinia pestis CO92
Authors: Nocek, B. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fumarylacetoacetate hydrolase family protein
B: Putative fumarylacetoacetate hydrolase family protein
C: Putative fumarylacetoacetate hydrolase family protein
D: Putative fumarylacetoacetate hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,03510
Polymers97,5204
Non-polymers5166
Water11,205622
1
A: Putative fumarylacetoacetate hydrolase family protein
D: Putative fumarylacetoacetate hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0836
Polymers48,7602
Non-polymers3244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-65 kcal/mol
Surface area16290 Å2
MethodPISA
2
B: Putative fumarylacetoacetate hydrolase family protein
C: Putative fumarylacetoacetate hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9524
Polymers48,7602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-49 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.169, 92.143, 157.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative fumarylacetoacetate hydrolase family protein / Putative fumarylacetoacetate hydrolase family protein


Mass: 24379.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: y2229 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q8D0F9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 315r / Detector: CCD / Date: Apr 10, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→37 Å / Num. all: 59586 / Num. obs: 55688 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12
Reflection shellResolution: 2→2.03 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
ARP/wARPmodel building
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.012→36.801 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2646 5.07 %
Rwork0.1602 --
obs0.1629 52175 86.86 %
all-54821 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.67 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0891 Å2-0 Å2-0 Å2
2---2.0805 Å20 Å2
3----3.0086 Å2
Refinement stepCycle: LAST / Resolution: 2.012→36.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 26 622 7133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086653
X-RAY DIFFRACTIONf_angle_d1.2519028
X-RAY DIFFRACTIONf_dihedral_angle_d13.5142452
X-RAY DIFFRACTIONf_chiral_restr0.0891026
X-RAY DIFFRACTIONf_plane_restr0.0071175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0123-2.04890.29031200.21731994X-RAY DIFFRACTION67
2.0489-2.08830.32161170.19932390X-RAY DIFFRACTION81
2.0883-2.13090.28481270.19812446X-RAY DIFFRACTION83
2.1309-2.17730.25461330.17652499X-RAY DIFFRACTION84
2.1773-2.22790.23961530.1742465X-RAY DIFFRACTION84
2.2279-2.28360.21181300.16472533X-RAY DIFFRACTION85
2.2836-2.34530.24251400.16332554X-RAY DIFFRACTION86
2.3453-2.41430.23421320.16282573X-RAY DIFFRACTION87
2.4143-2.49230.23471230.16362642X-RAY DIFFRACTION88
2.4923-2.58130.23571420.17292630X-RAY DIFFRACTION88
2.5813-2.68460.22831340.16482700X-RAY DIFFRACTION90
2.6846-2.80680.22341380.16322701X-RAY DIFFRACTION91
2.8068-2.95470.21451460.172718X-RAY DIFFRACTION91
2.9547-3.13970.19881530.16182772X-RAY DIFFRACTION92
3.1397-3.3820.2191520.15882803X-RAY DIFFRACTION93
3.382-3.7220.21231460.14482786X-RAY DIFFRACTION92
3.722-4.25990.16061530.13222787X-RAY DIFFRACTION91
4.2599-5.36440.13571470.12592746X-RAY DIFFRACTION89
5.3644-36.8070.22281600.18142790X-RAY DIFFRACTION87
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)
10.12930.17740.06540.31220.20820.27880.06870.06780.05870.0185-0.08640.05870.09220.04340.0280.04730.015-0.0130.06720.00060.076734.729638.8774-17.7575
20.15260.04-0.00710.0366-0.02230.0888-0.01780.00410.05780.0029-0.00830.0189-0.1090.05380.01320.0869-0.03-0.0050.0879-0.00590.070143.930447.5404-10.1374
30.39720.1160.07530.11170.17340.37120.1119-0.0027-0.0223-0.09130.00160.0127-0.2129-0.0029-0.04580.1534-0.01050.02790.0832-0.00470.095441.345155.6125-21.2414
40.14260.0360.01790.05680.07430.10790.0875-0.0071-0.0270.083-0.0138-0.0381-0.06470.0019-0.03180.08590.00420.02640.05850.02010.092136.023234.4075-10.2501
50.08420.00290.00470.0298-0.08510.27640.0387-0.0502-0.13720.0807-0.09410.02340.050.0250.02170.1256-0.01490.01610.06860.01080.120139.021131.8372-8.8992
60.1827-0.19340.01020.20490.00320.4163-0.0134-0.01430.0664-0.0436-0.1204-0.0739-0.0605-0.01450.02370.1095-0.04650.00640.0597-0.01450.122843.409959.3072-8.0442
70.19320.0640.06770.35490.03690.0320.0534-0.03350.0488-0.0549-0.07620.07280.0294-0.07840.00370.1223-0.01950.00320.09090.01040.09937.493146.9217-15.2816
80.33030.06980.01850.1083-0.04760.4036-0.07990.0626-0.107-0.0149-0.0545-0.11540.15210.11720.03070.13080.02270.00910.11610.00010.126849.73835.9067-20.2156
90.18930.1598-0.11040.52050.10510.2936-0.1007-0.0472-0.0097-0.0764-0.0006-0.056-0.02490.04250.05350.1348-0.0137-0.01090.12250.04270.192555.370647.7706-23.7037
100.09850.00910.05820.07710.06320.07380.01960.0418-0.03280.0329-0.04130.00650.02120.0561-0.03420.0637-0.0016-0.01040.080.01510.065543.315839.7488-8.3957
110.31930.04080.18331.06770.30240.17810.00430.21820.0132-0.2558-0.0151-0.0236-0.11110.1082-0.02540.14410.04180.01140.1927-0.01080.063547.820845.2584-27.9717
120.06470.0153-0.00040.06670.00240.00010.01260.12820.0332-0.07440.06730.02890.04860.0003-0.03520.17550.0556-0.03860.2655-0.00390.104343.362647.3451-30.6116
130.47040.1470.63670.20030.18821.1335-0.12560.08170.0499-0.0239-0.02660.0173-0.13830.0773-0.11030.088-0.0153-0.12540.1517-0.14470.272526.072625.006623.022
140.26380.0644-0.00490.04870.07690.17720.00220.0075-0.06290.0620.001-0.04990.082-0.04890.02140.1613-0.03380.00680.1095-0.02150.085237.41427.098632.9888
150.07130.0596-0.00730.0524-0.01530.03550.0090.0224-0.00840.02410.0137-0.00360.0250.0127-0.02470.7005-0.1982-0.0150.751-0.05540.478544.991913.993543.6208
160.0739-0.06970.05480.0998-0.04790.0452-0.0266-0.0646-0.00720.02770.0258-0.0169-0.00910.05750.00530.360.0682-0.11160.4019-0.02840.234948.610327.760645.962
170.11940.00530.00510.05730.04010.0937-0.11170.0135-0.0506-0.0503-0.03260.0338-0.0049-0.0854-0.0050.1013-0.03330.02340.1256-0.04460.126638.193220.717824.7292
180.03760.06520.0210.1915-0.06320.2187-0.0437-0.0386-0.0056-0.04780.0240.12550.12480.0277-0.00490.1156-0.03620.04810.1565-0.03360.123539.939718.744829.5911
190.257-0.2338-0.2670.54170.15080.4644-0.04680.0659-0.0280.1252-0.02070.01110.015-0.16070.03230.11470.03090.01360.152-0.06370.162332.365538.044940.7804
200.3162-0.0878-0.10860.11090.05090.1992-0.03940.00540.01150.1197-0.0450.06280.1601-0.04760.04730.1432-0.00890.04360.1334-0.0170.182645.210116.994631.602
210.03310.0690.07310.21360.08120.2573-0.08890.03110.04350.0368-0.06370.16490.02410.0052-0.0080.0792-0.01550.0420.1185-0.03270.140942.198521.808729.1855
220.21970.08490.04150.1557-0.02080.30820.0368-0.0739-0.08190.0244-0.0101-0.00930.1658-0.09180.05540.274-0.12260.1440.2295-0.05270.201130.368212.463838.7652
230.2231-0.0954-0.02290.19390.12480.1497-0.0473-0.08330.06980.09640.0498-0.04760.1806-0.09880.02580.1162-0.01830.01260.1126-0.03570.079338.48425.870738.6322
240.08990.0586-0.02650.0457-0.03760.05690.02840.0045-0.01250.0575-0.01280.02580.0624-0.05330.07810.2171-0.13230.1070.1716-0.07570.179830.53858.600827.7621
250.0509-0.0323-0.03530.08060.03710.07140.02550.02230.0261-0.0764-0.0291-0.03850.02480.02850.00750.08470.01980.0060.08380.00880.070147.30841.038415.7249
260.93410.06560.37630.99080.11920.16010.0055-0.0682-0.02150.3071-0.0237-0.2019-0.0271-0.0594-0.01950.1355-0.0073-0.02730.2003-0.00540.123669.060931.454227.0582
270.1793-0.05130.01480.25020.00480.16030.04-0.04540.0463-0.0852-0.03650.02380.03340.043-0.00760.099-0.0030.01130.0847-0.0120.087752.955435.337323.3515
280.0789-0.0991-0.04850.2151-0.01410.1524-0.02950.0144-0.00230.2091-0.05250.1147-0.04980.02580.01350.171-0.0070.01740.1209-0.0160.101155.293242.601828.3464
290.1428-0.05050.04870.176-0.20570.3029-0.0330.0767-0.0276-0.0745-0.07960.06050.08270.10490.01310.17480.0007-0.0260.0935-0.00310.069850.562625.60096.6193
300.3262-0.0639-0.12460.5612-0.18330.12930.0086-0.18-0.08810.13960.01370.018-0.0590.0407-0.02030.0668-0.014-0.0060.1098-0.01080.100855.225939.245714.8311
310.17830.0835-0.06460.1096-0.05640.28350.0571-0.0034-0.06670.0647-0.0398-0.0179-0.09880.04850.00750.1515-0.0045-0.01040.1806-0.02620.101158.444131.486437.4915
320.02680.0058-0.00970.0160.03590.15420.0128-0.0245-0.00940.0402-0.07120.032-0.0775-0.0113-0.00630.1069-0.0330.01830.09-0.01340.075252.064438.17624.824
330.1362-0.07070.09780.0394-0.05060.07240.03-0.04860.0594-0.03690.0252-0.06280.02850.09290.00130.0749-0.0210.01580.1875-0.0110.138663.463740.65078.6068
340.41660.16420.07450.1846-0.18010.4055-0.0378-0.0131-0.02520.0123-0.0385-0.0564-0.0450.02860.01940.126-0.0370.0230.1689-0.04760.138367.730648.775525.5073
350.1271-0.11630.05420.13580.01870.22080.06620.05670.0246-0.0416-0.0420.0630.12250.1073-0.01170.08410.00430.01260.0995-0.01030.090557.03529.580715.7679
360.0842-0.06630.07330.2231-0.19290.6257-0.0029-0.10910.08990.08810.0214-0.1412-0.260.0519-0.05110.2029-0.04860.04380.1702-0.05920.15260.976350.278925.0177
370.1922-0.2003-0.02450.3507-0.00510.01030.0259-0.0492-0.08810.0159-0.0184-0.09820.0478-0.00830.01760.0874-0.07780.0040.1610.01810.405713.483643.0318-4.8119
380.2425-0.0023-0.08670.1909-0.14580.16310.0597-0.16410.10020.15950.04310.2388-0.0982-0.05340.0480.088-0.00460.05030.0798-0.00760.155421.163452.4387-3.0887
390.55470.1981-0.0240.3050.00430.14260.1054-0.08410.06060.03610.00240.08640.0783-0.0974-0.04010.1231-0.01720.04620.16410.03220.158725.283545.3759.8445
400.0768-0.03910.08610.0652-0.11350.2704-0.08660.09150.09390.0537-0.01560.0294-0.1458-0.0156-0.0030.10910.0650.04360.14180.04490.183118.801859.8591-11.5664
410.01870.02510.00670.05210.03650.0493-0.02560.09460.06110.0503-0.02340.08840.0082-0.0298-0.02190.06570.06820.09420.17130.05040.223213.081458.1215-7.4512
420.5613-0.0059-0.03380.43590.04360.2867-0.0194-0.03260.01810.1312-0.00690.041-0.01470.0522-0.00450.155-0.00870.03420.1606-0.02970.169332.279351.65697.7325
430.035-0.04140.02840.0521-0.0380.044-0.0268-0.02430.02230.0877-0.00550.0270.02770.0658-0.00570.12-0.020.02560.1216-0.01550.081835.83250.35362.0062
440.18980.00560.00110.0783-0.04250.02890.128-0.02510.15410.07090.05410.1529-0.197-0.04220.05340.1410.08580.16370.1490.06780.292312.074657.61613.0182
450.0481-0.0026-0.0020.006-0.00920.03260.01250.00960.00060.03580.05770.0332-0.05020.0166-0.01880.1871-0.00920.0720.1332-0.06380.268918.010158.810616.15
460.0603-0.06710.02450.0796-0.02880.00910.05540.03970.07950.0809-0.03150.1282-0.04620.0109-0.09310.12770.12890.1686-0.1076-0.04360.241921.376265.8286-4.0507
470.21530.02910.01080.018-0.05450.21180.08810.01770.14380.10250.03370.1927-0.17040.0307-0.06030.1495-0.02570.04960.0851-0.01130.118224.241656.5646-3.1811
480.1497-0.068-0.08310.11160.00190.20540.0828-0.14330.1050.136-0.01360.06920.0285-0.0035-0.00360.2411-0.01640.16390.1989-0.01510.239613.837849.497212.4679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:27)
2X-RAY DIFFRACTION2(chain A and resid 28:55)
3X-RAY DIFFRACTION3(chain A and resid 56:71)
4X-RAY DIFFRACTION4(chain A and resid 72:82)
5X-RAY DIFFRACTION5(chain A and resid 83:101)
6X-RAY DIFFRACTION6(chain A and resid 102:116)
7X-RAY DIFFRACTION7(chain A and resid 117:136)
8X-RAY DIFFRACTION8(chain A and resid 137:152)
9X-RAY DIFFRACTION9(chain A and resid 153:158)
10X-RAY DIFFRACTION10(chain A and resid 159:198)
11X-RAY DIFFRACTION11(chain A and resid 199:211)
12X-RAY DIFFRACTION12(chain A and resid 212:218)
13X-RAY DIFFRACTION13(chain B and resid 1:12)
14X-RAY DIFFRACTION14(chain B and resid 13:27)
15X-RAY DIFFRACTION15(chain B and resid 28:34)
16X-RAY DIFFRACTION16(chain B and resid 35:41)
17X-RAY DIFFRACTION17(chain B and resid 42:60)
18X-RAY DIFFRACTION18(chain B and resid 61:80)
19X-RAY DIFFRACTION19(chain B and resid 81:94)
20X-RAY DIFFRACTION20(chain B and resid 95:112)
21X-RAY DIFFRACTION21(chain B and resid 113:137)
22X-RAY DIFFRACTION22(chain B and resid 138:161)
23X-RAY DIFFRACTION23(chain B and resid 162:198)
24X-RAY DIFFRACTION24(chain B and resid 199:218)
25X-RAY DIFFRACTION25(chain C and resid 2:24)
26X-RAY DIFFRACTION26(chain C and resid 25:36)
27X-RAY DIFFRACTION27(chain C and resid 37:55)
28X-RAY DIFFRACTION28(chain C and resid 56:77)
29X-RAY DIFFRACTION29(chain C and resid 78:91)
30X-RAY DIFFRACTION30(chain C and resid 92:101)
31X-RAY DIFFRACTION31(chain C and resid 102:116)
32X-RAY DIFFRACTION32(chain C and resid 117:136)
33X-RAY DIFFRACTION33(chain C and resid 137:147)
34X-RAY DIFFRACTION34(chain C and resid 148:159)
35X-RAY DIFFRACTION35(chain C and resid 160:192)
36X-RAY DIFFRACTION36(chain C and resid 193:218)
37X-RAY DIFFRACTION37(chain D and resid 1:6)
38X-RAY DIFFRACTION38(chain D and resid 7:54)
39X-RAY DIFFRACTION39(chain D and resid 55:70)
40X-RAY DIFFRACTION40(chain D and resid 71:90)
41X-RAY DIFFRACTION41(chain D and resid 91:99)
42X-RAY DIFFRACTION42(chain D and resid 100:110)
43X-RAY DIFFRACTION43(chain D and resid 111:127)
44X-RAY DIFFRACTION44(chain D and resid 128:153)
45X-RAY DIFFRACTION45(chain D and resid 154:158)
46X-RAY DIFFRACTION46(chain D and resid 159:176)
47X-RAY DIFFRACTION47(chain D and resid 177:198)
48X-RAY DIFFRACTION48(chain D and resid 199:218)

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