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- PDB-2hf0: Bifidobacterium longum bile salt hydrolase -

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Open data


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Basic information

Entry
Database: PDB / ID: 2hf0
TitleBifidobacterium longum bile salt hydrolase
ComponentsBile salt hydrolase
KeywordsHYDROLASE / alpha / beta
Function / homology
Function and homology information


chenodeoxycholoyltaurine hydrolase / chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase activity / choloylglycine hydrolase / bile acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase activity
Similarity search - Function
: / : / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuresh, C.G. / Kumar, R.S. / Brannigan, J.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Functional Analysis of a Conjugated Bile Salt Hydrolase from Bifidobacterium longum Reveals an Evolutionary Relationship with Penicillin V Acylase.
Authors: Kumar, R.S. / Brannigan, J.A. / Prabhune, A.A. / Pundle, A.V. / Dodson, G.G. / Dodson, E.J. / Suresh, C.G.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Bile salt hydrolase
B: Bile salt hydrolase


Theoretical massNumber of molelcules
Total (without water)70,1102
Polymers70,1102
Non-polymers00
Water4,522251
1
A: Bile salt hydrolase
B: Bile salt hydrolase

A: Bile salt hydrolase
B: Bile salt hydrolase


Theoretical massNumber of molelcules
Total (without water)140,2194
Polymers140,2194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area15050 Å2
ΔGint-103 kcal/mol
Surface area44110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.981, 123.981, 219.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, -y, z+3/2.

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Components

#1: Protein Bile salt hydrolase


Mass: 35054.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: bsh / Plasmid: pET 26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KK62, choloylglycine hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate 30% w/v, 0.5 M sodium formate, sucrose (1M) 100ml, 40 uL of b-octyl glucosidase (0.50% w/v), pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5148 Å
DetectorDetector: CCD / Date: Jan 30, 2004
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionResolution: 2.25→107.211 Å / Num. all: 48000 / Num. obs: 46662 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.25→2.3 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.94 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22835 2264 5.1 %RANDOM
Rwork0.18481 ---
obs0.18699 42515 99.74 %-
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 mean: 35.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 0 251 5177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0215027
X-RAY DIFFRACTIONr_bond_other_d0.0060.024263
X-RAY DIFFRACTIONr_angle_refined_deg2.11.9216837
X-RAY DIFFRACTIONr_angle_other_deg1.09639895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9455628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32424.196255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13815742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6121526
X-RAY DIFFRACTIONr_chiral_restr0.1960.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025794
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021090
X-RAY DIFFRACTIONr_nbd_refined0.2350.21089
X-RAY DIFFRACTIONr_nbd_other0.2320.24697
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22427
X-RAY DIFFRACTIONr_nbtor_other0.1030.22698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7091.53840
X-RAY DIFFRACTIONr_mcbond_other0.3471.51296
X-RAY DIFFRACTIONr_mcangle_it1.85725004
X-RAY DIFFRACTIONr_scbond_it3.15732286
X-RAY DIFFRACTIONr_scangle_it4.3194.51833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 154 -
Rwork0.237 3064 -
obs--99.94 %
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)
10.73440.35480.45011.83210.54520.34050.04690.2994-0.3503-0.3194-0.0306-0.15120.0970.0505-0.01630.1645-0.05750.01950.056-0.07010.077-46.26219.77183.4631
21.1171.6738-1.53756.158-0.34393.1689-0.0892-0.3138-0.29190.1470.0427-0.05130.5160.18880.04650.126-0.00940.02780.05860.02110.1342-41.726517.559924.8353
32.9981-0.1329-0.43920.88630.16660.0889-0.1026-0.1298-0.31880.0910.05210.23880.4027-0.33250.05050.2808-0.14030.0646-0.0173-0.06120.1436-54.22070.916115.6213
43.2339-3.6366-4.44634.08965.00016.11320.7141-1.2975-1.22781.1001-1.0326-0.75261.0035-0.07960.31850.3649-0.2253-0.0075-0.0767-0.11460.1056-55.52750.60016.0876
54.8533.2382-0.25674.3259-0.51828.86770.0348-0.3292-0.56790.5230.02670.53240.5117-0.3087-0.06150.2608-0.02670.0787-0.0432-0.04520.1896-48.54673.761619.9291
61.0972-1.4294-1.29621.89071.47573.1243-0.0402-0.0178-0.2833-0.090.0552-0.00490.3823-0.0152-0.01510.1695-0.10920.01810.0466-0.02630.122-52.265214.769416.3163
73.1177-1.5690.22454.23850.94881.76050.03570.016-0.50460.16440.03120.38840.3417-0.483-0.06690.1711-0.18910.02350.1060.04290.1102-67.492510.962422.6434
85.58370.9135.27422.0139-0.66696.2362-0.0666-0.1105-0.3322-0.16720.09290.17130.38520.0831-0.02630.2279-0.13630.03730.0536-0.03020.1202-57.26767.202514.9868
92.2949-1.6559-1.65697.2173-1.24522.18540.29090.3239-0.3482-0.3773-0.26960.23860.278-0.2873-0.02140.2083-0.1594-0.08030.097-0.08660.0732-61.447512.53015.0332
109.7188-3.3102-0.80326.22082.08710.71210.54910.92520.0783-0.8503-0.02880.5484-0.229-1.6799-0.5203-0.0994-0.61450.0022-0.12780.026-0.3835-66.357313.070217.8758
116.5278-2.28027.13399.0769-4.83988.462-0.2924-0.8096-0.19030.85090.52650.0219-0.4108-0.5776-0.23410.2012-0.03950.06630.11070.07640.1276-57.083312.461333.4085
121.28-0.0721-1.04790.80390.52884.77590.02490.0336-0.1081-0.07870.13990.27780.0442-0.391-0.16480.1265-0.1102-0.02370.0644-0.00760.0722-59.414120.914713.8355
131.8433-0.8844-0.5911.7769-0.70441.780.01470.1275-0.1788-0.02450.04450.20940.1746-0.3407-0.05930.0721-0.0576-0.01160.0795-0.02950.0446-55.081832.31813.1251
140.20680.5498-0.26721.9955-1.29150.9779-0.02470.29680.1336-0.1822-0.0597-0.1706-0.09520.08630.08440.1127-0.0173-0.00220.1155-0.01520.0789-41.435646.19212.2954
151.64830.90870.25430.53910.35351.23130.06810.24240.2651-0.2718-0.137-0.2126-0.13430.06290.06880.056-0.00940.01420.08920.00330.0547-35.50555.89015.9182
160.6350.0085-0.50820.2068-0.41711.22090.00110.0606-0.018-0.0486-0.0027-0.03780.0879-0.03470.00160.074-0.01310.00920.0619-0.01940.0454-44.127235.214512.2005
175.259312.22182.597128.97269.156118.3417-0.386-0.143-0.25130.45740.04140.87280.4258-0.50210.34460.1158-0.0250.04520.0703-0.07080.0617-39.953324.9837-3.9993
182.0788-0.3185-0.50682.3010.33090.152-0.04210.0781-0.3281-0.11270.0139-0.21150.36990.11780.02820.1437-0.01860.04320.0399-0.02360.0867-38.046922.85186.9509
190.59190.12170.07811.43771.0411.7215-0.02860.151-0.2844-0.0499-0.0217-0.05130.36470.00150.05030.154-0.01050.03160.0291-0.00750.1172-38.431716.990616.866
201.34811.4419-0.60716.01421.1243.8216-0.03450.031-0.42390.01570.1148-0.45520.24970.158-0.08020.2755-0.0080.0619-0.0047-0.05940.1857-43.1782-2.374113.7373
212.6497-0.75861.90112.7417-0.81764.0135-0.02280.073-0.29730.093-0.081-0.18570.24050.32650.10390.07450.02470.04890.1037-0.01450.1523-20.485532.256819.2884
228.99892.8048-0.91441.62270.80571.6823-0.12550.4411-0.0124-0.0459-0.1012-0.1789-0.09080.11570.22670.14290.08550.14240.044-0.08430.1888-10.818327.86195.7811
230.109-0.8221-0.07786.20110.58680.05550.03230.1149-0.287-0.3712-0.0789-0.92560.25870.7550.0466-0.07260.04320.1050.21220.02180.28512.645237.81748.74
2443.28931.8865-13.34048.21666.083413.53510.49691.08850.17940.3690.0288-0.5062-0.42060.9766-0.52570.05370.0772-0.03460.1270.11020.24111.635831.242117.8417
253.86741.169-4.23052.04121.29788.56030.05930.56650.0527-0.33990.1089-0.4714-0.32490.4135-0.16820.11770.06780.09090.1881-0.03660.2328-7.497931.12844.2289
260.90470.3879-0.50241.5097-0.48071.4006-0.03960.0367-0.1867-0.0873-0.029-0.29190.13010.37520.06860.03290.01690.03410.1286-0.01060.1088-9.038141.979310.7389
273.16350.0863-1.35541.9588-2.62015.8324-0.0057-0.1264-0.06310.2845-0.0617-0.2943-0.0550.51850.0674-0.00460.0256-0.02970.2018-0.00140.1494-4.202242.348521.7909
281.56930.7943-1.83612.8837-1.27449.4513-0.20560.5737-0.2762-0.37450.18680.17870.40940.12890.01880.0341-0.01420.05170.1581-0.03010.1689-9.259747.27720.8922
291.40050.6964-0.11041.7283-1.98344.49570.0227-0.0040.00690.06740.0175-0.1935-0.09260.2479-0.04020.02870.01180.03410.1108-0.00820.1233-14.841545.949616.5326
302.1822-0.7329-0.70711.49520.30342.0122-0.0188-0.095-0.05110.1294-0.0302-0.1171-0.03190.10290.0490.0438-0.0109-0.00410.0525-0.00870.0685-27.650647.000221.8293
318.865-0.9993-4.2885.28980.37049.362-0.1187-0.2605-0.02280.1949-0.02060.05450.0563-0.43410.13930.0771-0.01990.0070.0915-0.0010.0118-43.341135.558433.559
322.0532-0.8527-0.3041.4834-0.18390.7264-0.0978-0.2047-0.030.33980.04140.17140.0565-0.22120.05640.0703-0.0320.01230.0873-0.00710.0363-52.670538.805330.9951
335.31011.7877-8.56441.2973-2.989514.25470.0878-0.08220.13320.18760.0850.04010.0904-0.1726-0.17280.0743-0.008-0.00970.0722-0.00050.0658-38.870341.174317.0137
341.54740.4994-1.33142.6548-2.85683.50790.0518-0.0133-0.1337-0.0145-0.0255-0.02790.2053-0.0072-0.02630.06810.0031-0.00610.053-0.01710.0595-31.129738.423121.4553
3512.5773-1.5876-1.68836.6394-4.26383.3393-0.2488-0.40440.17550.3970.3377-0.6197-0.0340.3786-0.0890.08510.0009-0.03170.040.01920.1049-25.153925.894931.996
361.22770.8629-0.56531.5395-0.6430.89810.0119-0.1586-0.28260.0626-0.0214-0.29180.31190.19380.00940.10020.02250.02440.0446-0.00380.1194-25.840926.430221.6153
372.69570.03340.20694.6204-0.7983.96950.08940.36090.0594-0.4334-0.1337-0.42680.10410.32390.04430.1129-0.00470.04860.0928-0.03670.0904-33.837936.4671.6948
383.2480.25842.20260.5020.4393.3280.07880.0935-0.3563-0.0747-0.0256-0.23170.38220.2219-0.05320.1050.03760.06690.0571-0.01430.1311-21.278225.049112.5208
390.4517-0.1688-0.77962.3281-1.53872.82390.015-0.2098-0.3448-0.1459-0.0202-0.69570.3460.44260.00520.11920.08170.0570.1165-0.03820.2666-4.753120.05513.283
406.0924-0.6675-0.90671.1796-0.23473.561-0.2762-1.13710.4298-0.1493-0.07370.46620.1589-0.08440.350.0960.10680.15460.0195-0.07980.1768-7.263622.31834.1069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 161 - 16
2X-RAY DIFFRACTION2AA17 - 2617 - 26
3X-RAY DIFFRACTION3AA27 - 4827 - 48
4X-RAY DIFFRACTION4AA49 - 5249 - 52
5X-RAY DIFFRACTION5AA53 - 6353 - 63
6X-RAY DIFFRACTION6AA64 - 8664 - 86
7X-RAY DIFFRACTION7AA87 - 10187 - 101
8X-RAY DIFFRACTION8AA102 - 111102 - 111
9X-RAY DIFFRACTION9AA112 - 121112 - 121
10X-RAY DIFFRACTION10AA122 - 129122 - 129
11X-RAY DIFFRACTION11AA130 - 138130 - 138
12X-RAY DIFFRACTION12AA139 - 163139 - 163
13X-RAY DIFFRACTION13AA164 - 186164 - 186
14X-RAY DIFFRACTION14AA187 - 197187 - 197
15X-RAY DIFFRACTION15AA198 - 210198 - 210
16X-RAY DIFFRACTION16AA211 - 236211 - 236
17X-RAY DIFFRACTION17AA237 - 240237 - 240
18X-RAY DIFFRACTION18AA241 - 257241 - 257
19X-RAY DIFFRACTION19AA258 - 304258 - 304
20X-RAY DIFFRACTION20AA305 - 316305 - 316
21X-RAY DIFFRACTION21BB1 - 221 - 22
22X-RAY DIFFRACTION22BB23 - 3523 - 35
23X-RAY DIFFRACTION23BB36 - 4836 - 48
24X-RAY DIFFRACTION24BB49 - 5249 - 52
25X-RAY DIFFRACTION25BB53 - 6353 - 63
26X-RAY DIFFRACTION26BB64 - 10964 - 109
27X-RAY DIFFRACTION27BB110 - 124110 - 124
28X-RAY DIFFRACTION28BB125 - 136125 - 136
29X-RAY DIFFRACTION29BB137 - 163137 - 163
30X-RAY DIFFRACTION30BB164 - 189164 - 189
31X-RAY DIFFRACTION31BB190 - 195190 - 195
32X-RAY DIFFRACTION32BB196 - 213196 - 213
33X-RAY DIFFRACTION33BB214 - 221214 - 221
34X-RAY DIFFRACTION34BB222 - 236222 - 236
35X-RAY DIFFRACTION35BB237 - 240237 - 240
36X-RAY DIFFRACTION36BB241 - 256241 - 256
37X-RAY DIFFRACTION37BB257 - 270257 - 270
38X-RAY DIFFRACTION38BB271 - 298271 - 298
39X-RAY DIFFRACTION39BB299 - 309299 - 309
40X-RAY DIFFRACTION40BB310 - 316310 - 316

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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