[English] 日本語
Yorodumi
- PDB-2gvh: Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gvh
TitleCrystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTERIUM TUMEFACIENS at 2.65 A resolution
ComponentsAGR_L_2016p
KeywordsHYDROLASE / 15159470 / Acyl-CoA hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty acid catabolic process / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTERIUM TUMEFACIENS at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AGR_L_2016p
B: AGR_L_2016p
C: AGR_L_2016p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9084
Polymers95,8853
Non-polymers231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-48 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.209, 121.209, 81.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C
161A
171B
181C
191A
201B
211C
221A
231B
241C
251A
261B
271C
281A
291B
301C
311A
321B
331C
341A
351B
361C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHE1AA9 - 6921 - 81
21PROPROPHEPHE1BB10 - 6922 - 81
31GLUGLUPHEPHE1CC8 - 6920 - 81
42ARGARGPROPRO2AA70 - 7282 - 84
52ARGARGPROPRO2BB70 - 7282 - 84
62ARGARGPROPRO2CC70 - 7282 - 84
73ALAALAHISHIS1AA73 - 7785 - 89
83ALAALAHISHIS1BB73 - 7785 - 89
93ALAALAHISHIS1CC73 - 7785 - 89
104ILEILEGLYGLY1AA78 - 8990 - 101
114ILEILEGLYGLY1BB78 - 8990 - 101
124ILEILEGLYGLY1CC78 - 8990 - 101
135ARGARGARGARG3AA90102
145ARGARGARGARG3BB90102
155ARGARGARGARG3CC90102
166ARGARGGLYGLY1AA91 - 125103 - 137
176ARGARGGLYGLY1BB91 - 125103 - 137
186ARGARGGLYGLY1CC91 - 125103 - 137
197GLUGLUTHRTHR4AA124 - 138136 - 150
207GLUGLUTHRTHR4BB124 - 138136 - 150
217GLUGLUTHRTHR4CC124 - 138136 - 150
228GLUGLUALAALA6AA139 - 147151 - 159
238GLUGLUALAALA6BB139 - 147151 - 159
248GLUGLUALAALA6CC139 - 147151 - 159
259VALVALGLYGLY1AA151 - 220163 - 232
269VALVALGLYGLY1BB151 - 220163 - 232
279VALVALGLYGLY1CC151 - 220163 - 232
2810ARGARGSERSER5AA221 - 225233 - 237
2910ARGARGSERSER5BB221 - 225233 - 237
3010ARGARGSERSER5CC221 - 225233 - 237
3111ILEILEASPASP1AA226 - 254238 - 266
3211ILEILEASPASP1BB226 - 254238 - 266
3311ILEILEASPASP1CC226 - 254238 - 266
3412ARGARGILEILE1AA258 - 262270 - 274
3512ARGARGILEILE1BB258 - 262270 - 274
3612ARGARGILEILE1CC258 - 262270 - 274

-
Components

#1: Protein AGR_L_2016p


Mass: 31961.771 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: 15159470 / Production host: Escherichia coli (E. coli)
References: GenBank: 15159470, UniProt: Q7CTE6*PLUS, acyl-CoA hydrolase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.133836 Å3/Da / Density % sol: 60.750973 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 10.0% iso-Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2005 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.5→48.7 Å / Num. obs: 35343 / % possible obs: 86.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.625 Å2 / Rmerge(I) obs: 0.096 / Χ2: 1.051 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2% possible all
2.5-2.5955.12.50.50822440.95555.1
2.59-2.6963.12.90.47725861.014
2.69-2.8270.83.20.39328911.018
2.82-2.9682.13.40.30933391.054
2.96-3.1590.73.60.2337151.044
3.15-3.39993.70.16940591.138
3.39-3.731003.80.1240911.095
3.73-4.2799.93.80.08641110.958
4.27-5.3999.63.80.06941041.002
5.39-9999.53.70.08142031.133

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.06 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.264
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. THE FOLLOWING AREAS HAVE POOR DENSITIES: 73-77, 138-147, 221-225, 254-262. DENSITY FOR LOOPS BETWEEN 138-147, 254-262 ISN'T OF SUFFICIENT QUALITY TO ASSIGN MAIN CHAIN AND SIDE CHAIN ...Details: 1. THE FOLLOWING AREAS HAVE POOR DENSITIES: 73-77, 138-147, 221-225, 254-262. DENSITY FOR LOOPS BETWEEN 138-147, 254-262 ISN'T OF SUFFICIENT QUALITY TO ASSIGN MAIN CHAIN AND SIDE CHAIN POSITIONS RELIABLY, SO REGISTER ERRORS MAY BE PRESENT IN THE CURRENT MODEL IN THESE PLACES. 2. THE NOMINAL RESOLUTION IS 2.65 A WITH 3679 OBSERVED REFLECTIONS BETWEEN 2.65-2.50 (57.6% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1773 5 %RANDOM
Rwork0.226 ---
all0.227 ---
obs0.22663 35321 86.07 %-
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: 66.083 Å2
Baniso -1Baniso -2Baniso -3
1--5.13 Å20 Å20 Å2
2---5.13 Å20 Å2
3---10.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5443 0 1 0 5444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225545
X-RAY DIFFRACTIONr_angle_refined_deg1.411.947530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0555740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57522.108204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31115823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2271542
X-RAY DIFFRACTIONr_chiral_restr0.080.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024157
X-RAY DIFFRACTIONr_nbd_refined0.2260.22224
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2160
X-RAY DIFFRACTIONr_metal_ion_refined0.190.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.25
X-RAY DIFFRACTIONr_mcbond_it1.54933694
X-RAY DIFFRACTIONr_mcangle_it2.77955876
X-RAY DIFFRACTIONr_scbond_it5.35571874
X-RAY DIFFRACTIONr_scangle_it6.94991654
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1576TIGHT POSITIONAL0.050.05
2B1576TIGHT POSITIONAL0.060.05
3C1576TIGHT POSITIONAL0.060.05
1A123MEDIUM POSITIONAL0.30.5
2B123MEDIUM POSITIONAL0.480.5
3C123MEDIUM POSITIONAL0.350.5
1A48LOOSE POSITIONAL0.945
2B48LOOSE POSITIONAL1.175
3C48LOOSE POSITIONAL1.665
1A1576TIGHT THERMAL0.140.5
2B1576TIGHT THERMAL0.170.5
3C1576TIGHT THERMAL0.160.5
1A123MEDIUM THERMAL1.312
2B123MEDIUM THERMAL1.732
3C123MEDIUM THERMAL1.212
1A48LOOSE THERMAL9.7110
2B48LOOSE THERMAL8.4610
3C48LOOSE THERMAL6.2510
LS refinement shellResolution: 2.5→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 86 -
Rwork0.337 1559 -
obs-1645 54.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2672-0.9121-0.64362.8775-0.74540.9846-0.0981-0.2978-0.4190.33410.0549-0.04950.09170.09920.04320.06740.02780.0655-0.04830.1155-0.110742.618814.13818.8651
22.3143-0.2785-0.60213.0992-0.38140.9987-0.06910.0561-0.4999-0.2085-0.1343-0.38270.23690.12410.2034-0.04630.02140.1231-0.06970.0025-0.141861.178220.4389-4.2218
32.4754-0.3682-0.92721.3359-0.25161.12810.0660.24680.0175-0.0592-0.06310.1449-0.1227-0.0998-0.0029-0.10.02840.0219-0.13330.0119-0.291738.123339.0392.1972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA9 - 14321 - 155
21CC147 - 262159 - 274
32BB10 - 14322 - 155
42AA147 - 262159 - 274
53CC7 - 14319 - 155
63BB144 - 262156 - 274

+
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