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- PDB-6ok1: Ltp2-ChsH2(DUF35) aldolase -

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Basic information

Entry
Database: PDB / ID: 6ok1
TitleLtp2-ChsH2(DUF35) aldolase
Components
  • ChsH2(DUF35)
  • Lipid-transfer protein
KeywordsTRANSPORT PROTEIN / Aldolase / cholesterol degradation / thiolase superfamily / DUF35 domain
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Oxo-acid-lyases / bile acid catabolic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / acyltransferase activity, transferring groups other than amino-acyl groups / lipid catabolic process / lyase activity
Similarity search - Function
Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / HotDog domain superfamily ...Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / HotDog domain superfamily / Thiolase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Steroid side-chain-cleaving aldolase / Probable enoyl-CoA hydratase alpha subunit
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKimber, M.S. / Mallette, E. / Aggett, R. / Seah, S.Y.K.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The steroid side-chain-cleaving aldolase Ltp2-ChsH2DUF35is a thiolase superfamily member with a radically repurposed active site.
Authors: Aggett, R. / Mallette, E. / Gilbert, S.E. / Vachon, M.A. / Schroeter, K.L. / Kimber, M.S. / Seah, S.Y.K.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid-transfer protein
B: ChsH2(DUF35)
C: Lipid-transfer protein
D: ChsH2(DUF35)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,95220
Polymers115,6004
Non-polymers1,35216
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-143 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.680, 110.560, 120.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Lipid-transfer protein


Mass: 42997.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_3479 / Plasmid: pTIPQC2 / Production host: Rhodococcus jostii RHA1 (bacteria) / Strain (production host): Rha1 / References: UniProt: D1AB74
#2: Protein ChsH2(DUF35)


Mass: 14803.011 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_3482 / Plasmid: pTIPRT2 / Production host: Rhodococcus jostii RHA1 (bacteria) / References: UniProt: D1AB77

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Non-polymers , 6 types, 883 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium thiocyanate, 20% PEG 3350, 16 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 134309 / % possible obs: 99.92 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0485 / Net I/σ(I): 19.08
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 11051 / CC1/2: 0.734 / Rsym value: 0.724 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→42.828 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.48
RfactorNum. reflection% reflection
Rfree0.168 6714 5 %
Rwork0.1443 --
obs0.1455 134294 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7707 0 70 867 8644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088204
X-RAY DIFFRACTIONf_angle_d0.98511226
X-RAY DIFFRACTIONf_dihedral_angle_d13.3464928
X-RAY DIFFRACTIONf_chiral_restr0.0591233
X-RAY DIFFRACTIONf_plane_restr0.0081491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.262220.22664205X-RAY DIFFRACTION100
1.7193-1.73950.23572210.2134212X-RAY DIFFRACTION100
1.7395-1.76080.26922210.20754199X-RAY DIFFRACTION100
1.7608-1.78310.24532220.19984213X-RAY DIFFRACTION100
1.7831-1.80650.19632190.17874168X-RAY DIFFRACTION100
1.8065-1.83130.20692240.17754236X-RAY DIFFRACTION100
1.8313-1.85740.19812210.16914215X-RAY DIFFRACTION100
1.8574-1.88510.18462210.16654190X-RAY DIFFRACTION100
1.8851-1.91460.19712250.16684267X-RAY DIFFRACTION100
1.9146-1.9460.20652210.16074204X-RAY DIFFRACTION100
1.946-1.97950.2182210.15774195X-RAY DIFFRACTION100
1.9795-2.01550.19942240.15064259X-RAY DIFFRACTION100
2.0155-2.05430.17932200.14394189X-RAY DIFFRACTION100
2.0543-2.09620.15642240.13914246X-RAY DIFFRACTION100
2.0962-2.14180.18042220.13784222X-RAY DIFFRACTION100
2.1418-2.19160.19092240.13514251X-RAY DIFFRACTION100
2.1916-2.24640.15432220.12964226X-RAY DIFFRACTION100
2.2464-2.30720.17512240.134254X-RAY DIFFRACTION100
2.3072-2.37510.15732210.12674209X-RAY DIFFRACTION100
2.3751-2.45170.17972250.12794262X-RAY DIFFRACTION100
2.4517-2.53930.15842230.12414244X-RAY DIFFRACTION100
2.5393-2.6410.16732250.12684279X-RAY DIFFRACTION100
2.641-2.76120.1352250.12944264X-RAY DIFFRACTION100
2.7612-2.90670.15992240.13024258X-RAY DIFFRACTION100
2.9067-3.08880.18232250.14514285X-RAY DIFFRACTION100
3.0888-3.32720.14312260.14654280X-RAY DIFFRACTION100
3.3272-3.66190.15462270.14074322X-RAY DIFFRACTION100
3.6619-4.19130.16052280.13254331X-RAY DIFFRACTION100
4.1913-5.27910.14012300.12854365X-RAY DIFFRACTION100
5.2791-42.84190.17662370.17924530X-RAY DIFFRACTION100
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)
10.266-0.12110.13280.0330.0720.2414-0.11420.02280.1131-0.03050.05440.0314-0.17740.0097-0.0010.2937-0.0115-0.02440.1568-0.02450.2226-25.440614.3079-3.967
20.28490.1067-0.11030.0861-0.12510.1066-0.10030.06250.0562-0.04220.06640.0019-0.05410.05300.29670.0102-0.0120.2076-0.0440.2277-25.86236.1449-6.0106
30.43310.12480.19440.34340.14690.6452-0.0788-0.01690.07360.00890.01460.0599-0.0728-0.19630.00010.13990.04740.00930.1956-0.02790.1907-45.35552.1015-6.8307
40.1670.09620.12370.02860.00950.085-0.1298-0.01380.11350.04020.00520.1008-0.1935-0.1293-0.10050.25480.1174-0.03550.2115-0.04780.2927-45.132715.1752-4.9799
50.0145-0.0160.00360.01050.02240.00110.14860.2302-0.1798-0.06370.0304-0.21240.06160.13740.00010.21650.00760.01850.229-0.04220.265-28.2721-27.0253-4.4051
60.23680.1002-0.04380.20.05970.04910.0769-0.036-0.10330.0553-0.0393-0.00850.1164-0.091900.2059-0.04140.00650.19090.00520.1819-38.2713-24.92624.5509
70.0681-0.03820.06190.06810.03060.04930.12480.0439-0.0202-0.1635-0.04020.0990.03960.019900.257-0.02180.03340.2839-0.01450.2054-42.7618-20.2577-13.6035
8-0.0009-0.0004-0.00490.0020.00690.0041-0.0593-0.03080.0723-0.05130.03790.03630.0449-0.022800.2425-0.0569-0.00610.3417-0.03010.256-53.4454-22.9218-15.3375
90.0064-0.00420.01640.00410.00230.02140.04010.1073-0.0315-0.10810.10660.0150.1407-0.05540.00010.2687-0.0550.04610.2579-0.06370.2834-40.5354-31.4276-12.1385
100.00140.0081-0.00030.020.0227-0.0114-0.0547-0-0.0243-0.23920.0838-0.17430.0521-0.010500.2449-0.05960.00620.2315-0.02020.2889-43.354-30.6868-14.0704
110.0880.04820.05810.01320.00010.09110.0212-0.1068-0.04890.1012-0.0194-0.0448-0.0056-0.0293-00.24950.02790.00290.2318-0.03950.2073-19.2913-6.70316.2218
120.06170.00620.16470.08560.02580.2016-0.0199-0.0742-0.03020.0562-0.0024-0.0097-0.0416-0.0543-00.18350.01440.02010.1829-0.03620.1688-27.3498-4.657511.3926
130.13710.15130.15790.10430.030.1486-0.0685-0.10960.0068-0.01680.0751-0.0374-0.05470.10640.00020.2220.0160.01910.1851-0.03790.1848-20.9572-5.285.8501
140.4860.15160.11220.48880.14010.3171-0.0604-0.0501-0.05570.06650.0718-0.1461-0.08990.1126-00.1713-0.0049-0.00960.2338-0.05660.2261-3.1251-2.075510.6253
150.2034-0.05550.03310.1547-0.12050.0686-0.0919-0.03190.0808-0.01280.0697-0.0995-0.20130.1105-0.00390.2491-0.0531-0.02570.2226-0.07490.2252-4.189111.047611.0275
160.0282-0.0151-0.00530.0354-0.0180.0097-0.0149-0.0282-0.06750.01540.0427-0.0765-0.08270.1162-00.2462-0.0121-0.03260.2765-0.0480.216-2.4551-0.807220.2537
170.10830.06570.06530.05180.03620.0569-0.0114-0.09980.0680.115-0.0066-0.0683-0.14510.042600.29120.006-0.01740.2666-0.06050.212-13.17142.241423.1215
180.00540.00540.00090.0071-0.00270.0083-0.02250.0325-0.1143-0.04340.06180.10310.07090.103300.2989-0.0922-0.01310.3476-0.03290.2696-11.61514.3279-19.8025
190.0038-0.0038-0.0019-0.0016-0.00080.00590.00820.10580.0327-0.04140.07120.052-0.00910.0364-00.3494-0.16290.04980.5373-0.03660.2278-3.78518.1915-24.5587
20-0.0047-0.03240.02250.0629-0.09010.1194-0.17220.2080.2956-0.10040.0754-0.0156-0.44070.2632-0.05930.4125-0.1963-0.01750.32790.05770.2688-6.648419.322-18.3892
210.0702-0.0016-0.0090.03090.03310.232-0.10580.2886-0.0243-0.06450.1470.0079-0.03670.79110.020.2547-0.12680.03080.4242-0.10210.367.07223.5729-9.4523
220.0135-0.02770.03790.0894-0.09450.2216-0.04810.1856-0.10190.0214-0.0343-0.0391-0.13520.0811-0.00350.2118-0.14040.06620.5891-0.12810.500616.89795.1172-7.6662
230.0193-0.00850.00270.0378-0.00780.0105-0.05360.0329-0.1239-0.0905-0.16990.00870.05560.2534-0.07280.1649-0.32170.22350.8938-0.0740.31918.11534.8303-20.9253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:98 )A3 - 98
2X-RAY DIFFRACTION2( CHAIN A AND RESID 99:131 )A99 - 131
3X-RAY DIFFRACTION3( CHAIN A AND RESID 132:321 )A132 - 321
4X-RAY DIFFRACTION4( CHAIN A AND RESID 322:394 )A322 - 394
5X-RAY DIFFRACTION5( CHAIN B AND RESID 187:204 )B187 - 204
6X-RAY DIFFRACTION6( CHAIN B AND RESID 205:251 )B205 - 251
7X-RAY DIFFRACTION7( CHAIN B AND RESID 252:279 )B252 - 279
8X-RAY DIFFRACTION8( CHAIN B AND RESID 280:292 )B280 - 292
9X-RAY DIFFRACTION9( CHAIN B AND RESID 293:302 )B293 - 302
10X-RAY DIFFRACTION10( CHAIN B AND RESID 303:317 )B303 - 317
11X-RAY DIFFRACTION11( CHAIN C AND RESID 2:25 )C2 - 25
12X-RAY DIFFRACTION12( CHAIN C AND RESID 26:98 )C26 - 98
13X-RAY DIFFRACTION13( CHAIN C AND RESID 99:131 )C99 - 131
14X-RAY DIFFRACTION14( CHAIN C AND RESID 132:248 )C132 - 248
15X-RAY DIFFRACTION15( CHAIN C AND RESID 249:321 )C249 - 321
16X-RAY DIFFRACTION16( CHAIN C AND RESID 322:347 )C322 - 347
17X-RAY DIFFRACTION17( CHAIN C AND RESID 348:393 )C348 - 393
18X-RAY DIFFRACTION18( CHAIN D AND RESID 188:195 )D188 - 195
19X-RAY DIFFRACTION19( CHAIN D AND RESID 196:204 )D196 - 204
20X-RAY DIFFRACTION20( CHAIN D AND RESID 205:241 )D205 - 241
21X-RAY DIFFRACTION21( CHAIN D AND RESID 242:279 )D242 - 279
22X-RAY DIFFRACTION22( CHAIN D AND RESID 280:292 )D280 - 292
23X-RAY DIFFRACTION23( CHAIN D AND RESID 293:314 )D293 - 314

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