[English] 日本語
Yorodumi
- PDB-2jbw: Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jbw
TitleCrystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.
Components2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / META-CLEAVAGE PATHWAY / RETRO- FRIEDEL- CRAFTS ACYLATION / NICOTINE DEGRADATION / HYPOTHETICAL PROTEIN / PLASMID / CATALYTIC TRIAD / C-C BOND CLEAVAGE
Function / homology
Function and homology information


2,6-dihydroxypseudooxynicotine hydrolase / nicotine catabolic process / alkaloid metabolic process / hydrolase activity
Similarity search - Function
acylaminoacyl peptidase / Esterase FrsA-like / Esterase FrsA-like / de novo design (two linked rop proteins) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,6-dihydropseudooxynicotine hydrolase
Similarity search - Component
Biological speciesARTHROBACTER NICOTINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSchleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Action of a Cc Bond Cleaving Alpha/Beta-Hydrolase Involved in Nicotine Degration.
Authors: Schleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E.
History
DepositionDec 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
B: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
C: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
D: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,5388
Polymers175,4464
Non-polymers924
Water17,366964
1
A: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
B: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7694
Polymers87,7232
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
D: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7694
Polymers87,7232
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.570, 57.020, 152.697
Angle α, β, γ (deg.)90.00, 103.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A139 - 384
2115B139 - 384
1125A40 - 111
2125B40 - 111

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.421495, 0.102558, -0.901013), (0.109886, -0.992039, -0.061514), (-0.900149, -0.073081, -0.429409)157.0857, 48.1957, 253.293
2given(0.580614, 0.013364, -0.814069), (0.005988, -0.999908, -0.012143), (-0.814157, 0.002176, -0.580641)63.8634, 50.7271, 124.8256

-
Components

#1: Protein
2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE / DHPON-HYDROLASE


Mass: 43861.480 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER NICOTINOVORANS (bacteria) / Plasmid: PH6EX3.DHPONH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q93NG6, EC: 3.7.1.-
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.8
Details: PROTEINSOLUTION: 50 MM TRIS-HCL PH 7.4, 200 MM NACL, 0.5 M TCEP RESERVOIR: 35% PEG 10000, O.1 M TRIS-HCL PH 8.8 HANGING DROP, MIXED 1:1, MICROSEEDING

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 172409 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 98

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.26 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2580 2.9 %RANDOM
Rwork0.181 ---
obs0.183 86393 99.9 %-
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: 37.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-1.63 Å2
2--0.18 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11242 0 4 964 12210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02211517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.96915652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91951425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2424.133525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.836151927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9161572
X-RAY DIFFRACTIONr_chiral_restr0.1110.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.25855
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27767
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21068
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.57116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.333211417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40534637
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3284.54235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1904medium positional0.160.5
2288medium positional0.10.5
1850loose positional0.465
2302loose positional0.455
1904medium thermal1.42
2288medium thermal0.732
1850loose thermal2.1210
2302loose thermal1.4410
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 186
Rwork0.208 6256
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)
12.0628-0.32222.65483.73111.99584.34530.02680.091-0.0464-0.2393-0.062-0.5312-0.20230.13880.0352-0.0502-0.04150.00840.00650.0303-0.128784.75227.2414132.3267
224.32924.731-3.67919.742316.43927.861-0.70010.03660.76850.25330.7954-0.66880.52260.8039-0.0953-0.0528-0.0485-0.0260.08850.0539-0.157386.22433.6607125.75
315.38010.3647-1.42592.9060.154.8527-0.09450.42241.2259-0.2057-0.0803-0.4096-1.1259-0.01020.17480.170.0177-0.1121-0.1038-0.0368-0.18679.278441.4957133.7179
48.7295-1.21683.60171.2063-1.10642.98050.1776-0.51420.12820.062-0.2648-0.1117-0.4284-0.46340.08720.13860.0908-0.08950.0615-0.1463-0.159876.960436.0452139.5102
517.1142-2.0592-1.37941.1501-0.40219.7074-0.0879-0.18821.6104-0.1018-0.1291-0.3698-1.11020.58590.2170.1222-0.0284-0.1114-0.0627-0.0953-0.108883.686339.9627146.0872
62.2272-0.22321.34442.7884-0.6179.6638-0.0246-0.67470.18410.4501-0.25180.2771-0.8848-1.34920.2764-0.07970.09270.02350.2098-0.1734-0.229169.635133.6623152.5738
71.5496-1.44411.10863.33271.24034.0338-0.053-0.45490.00920.3697-0.11280.39490.2657-1.00780.1658-0.0569-0.10130.08990.339-0.0126-0.260170.287224.504152.6217
83.09232.32162.2823.4722.0983.9869-0.0893-0.3601-0.05710.2275-0.06270.23540.0513-0.68670.152-0.0387-0.01340.0550.1983-0.0066-0.227872.805223.9128147.4054
91.0498-0.9013-0.1421.34841.64691.524-0.1923-0.6439-0.00840.6948-0.04880.04180.1263-0.60010.24110.0736-0.04420.04810.36170.0041-0.343877.144525.0766160.5712
104.7871.4285-1.05571.17272.63211.9946-0.0858-0.7077-0.34010.539-0.0097-0.150.9164-0.65360.09550.1115-0.17030.02040.16310.1235-0.292878.242514.9043155.9425
113.7040.52650.7172.48180.62213.9016-0.0359-0.1994-0.0450.32560.1996-0.67220.13440.4081-0.1637-0.040.0174-0.1188-0.0551-0.0094-0.08996.488122.5207149.2701
122.9063-0.0672.34912.58051.0524.94520.2131-0.3664-0.30450.57350.1293-0.31640.90620.0127-0.34230.11660.0294-0.0838-0.04950.0831-0.213388.844911.1438151.879
133.5908-1.47052.39353.3322-2.12755.52980.311-0.2742-0.63960.3372-0.0814-0.12321.0084-0.2103-0.22970.1394-0.0781-0.0561-0.10780.0975-0.155383.97057.0061144.5282
149.69564.8333-3.25795.0748-4.278111.27770.2279-0.1155-0.77050.3597-0.21560.05020.8865-0.673-0.01230.0144-0.19310.0570.04920.0793-0.17870.959410.5045143.4769
1551.2325-18.6466-17.679514.57495.86929.0092-1.0619-1.9183-2.30550.60020.75540.38551.29570.09360.30660.2516-0.3034-0.1485-0.32870.0828-0.103677.4760.211144.9677
163.18381.80415.03782.08080.13245.38720.01110.3190.1072-0.0415-0.0686-0.1627-0.00510.61410.0575-0.11340.07090.02690.0582-0.0304-0.083876.555322.7097117.3385
177.54282.66370.68962.94760.65713.820.01380.1782-0.1783-0.30580.1085-0.17170.93920.4693-0.1223-0.0110.067-0.0513-0.0228-0.0969-0.069477.864810.3788119.0301
18-3.28411.1727-1.751520.67944.148732.97560.5785-0.2887-0.3047-0.12210.32931.08342.0331-0.65-0.90780.0186-0.280.0280.07880.0433-0.141264.77864.8101135.9422
191.80390.6360.28051.3206-2.976612.73440.2046-0.0139-0.2095-0.1161-0.19720.08110.6344-0.4818-0.0074-0.0179-0.0774-0.03010.0119-0.0836-0.09568.57513.6844117.4541
201.92590.1586-2.93274.29880.938816.35630.1301-0.0512-0.64080.1497-0.1785-0.00391.7634-0.80020.0484-0.0626-0.185-0.05320.0616-0.0441-0.105462.28349.1374117.6898
218.3874-1.593512.38675.3886-2.924831.98810.1937-0.9989-0.90230.2045-0.19670.49051.1346-2.27850.003-0.3766-0.1740.17510.6868-0.0871-0.217849.576814.9102122.994
222.86040.6847-0.59238.14534.625815.23950.0362-0.7206-0.01320.4761-0.50850.81290.5342-1.740.4722-0.3935-0.1080.08180.6453-0.1066-0.132448.545919.1857123.4101
232.1594-1.0237-0.10972.1886-0.01034.45170.057-0.364-0.11040.2031-0.380.0767-0.0546-0.8460.323-0.1940.01970.01550.3236-0.1056-0.158258.017823.7433120.5573
242.8281-1.3071.12773.04763.15927.1457-0.0188-0.526-0.1760.2297-0.25820.46690.1641-1.1430.277-0.19310.00270.07990.3088-0.0609-0.172455.387723.5874121.9382
251.1618-0.5352-1.3442.77950.66117.19060.1275-0.5111-0.2617-0.1405-0.17320.59350.3219-1.51720.0457-0.28080.0373-0.06270.4832-0.1513-0.099748.249721.3882110.3458
26-0.97160.87260.16673.0813-1.02965.11890.2424-0.4858-0.12480.2474-0.26580.5582-0.176-0.97150.0234-0.19850.18090.02230.4814-0.1587-0.162549.932129.5449120.3021
274.4774-0.54460.56441.052-1.84863.0610.0018-0.51020.1979-0.1122-0.04010.3029-0.4701-0.87090.0383-0.08650.285-0.06080.2395-0.2509-0.142252.993733.92111.8985
281.4686-0.06021.30251.46661.08613.7584-0.23340.04940.1335-0.1527-0.02250.0692-0.5602-0.09530.2559-0.04390.1507-0.05540.0131-0.0993-0.145662.411132.512103.3612
291.31970.41731.55650.5227-1.4953.4226-0.4074-0.43280.48790.1674-0.0238-0.1422-1.0468-0.47990.43130.08950.2654-0.08510.1323-0.213-0.110361.208939.4149120.3773
3044.033913.3557-35.89688.9936-14.530333.6313-0.595-0.02382.23680.25750.68340.8967-0.868-1.7511-0.08850.37680.3995-0.1536-0.0434-0.3919-0.231859.11347.792120.904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 28
2X-RAY DIFFRACTION2A29 - 35
3X-RAY DIFFRACTION3A36 - 60
4X-RAY DIFFRACTION4A61 - 89
5X-RAY DIFFRACTION5A90 - 100
6X-RAY DIFFRACTION6A101 - 122
7X-RAY DIFFRACTION7A123 - 149
8X-RAY DIFFRACTION8A150 - 176
9X-RAY DIFFRACTION9A177 - 208
10X-RAY DIFFRACTION10A209 - 237
11X-RAY DIFFRACTION11A238 - 272
12X-RAY DIFFRACTION12A273 - 306
13X-RAY DIFFRACTION13A307 - 336
14X-RAY DIFFRACTION14A337 - 350
15X-RAY DIFFRACTION15A351 - 366
16X-RAY DIFFRACTION16B6 - 28
17X-RAY DIFFRACTION17B29 - 55
18X-RAY DIFFRACTION18B56 - 66
19X-RAY DIFFRACTION19B67 - 89
20X-RAY DIFFRACTION20B90 - 108
21X-RAY DIFFRACTION21B109 - 120
22X-RAY DIFFRACTION22B121 - 137
23X-RAY DIFFRACTION23B138 - 158
24X-RAY DIFFRACTION24B159 - 178
25X-RAY DIFFRACTION25B179 - 203
26X-RAY DIFFRACTION26B204 - 221
27X-RAY DIFFRACTION27B222 - 245
28X-RAY DIFFRACTION28B246 - 309
29X-RAY DIFFRACTION29B310 - 351
30X-RAY DIFFRACTION30B352 - 365

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more