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- PDB-2gvh: Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTE... -

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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


thiolester hydrolase activity
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSPHE1AA9 - 6921 - 81
21PROPHE1BB10 - 6922 - 81
31GLUPHE1CC8 - 6920 - 81
42ARGPRO2AA70 - 7282 - 84
52ARGPRO2BB70 - 7282 - 84
62ARGPRO2CC70 - 7282 - 84
73ALAHIS1AA73 - 7785 - 89
83ALAHIS1BB73 - 7785 - 89
93ALAHIS1CC73 - 7785 - 89
104ILEGLY1AA78 - 8990 - 101
114ILEGLY1BB78 - 8990 - 101
124ILEGLY1CC78 - 8990 - 101
135ARGARG3AA90102
145ARGARG3BB90102
155ARGARG3CC90102
166ARGGLY1AA91 - 125103 - 137
176ARGGLY1BB91 - 125103 - 137
186ARGGLY1CC91 - 125103 - 137
197GLUTHR4AA124 - 138136 - 150
207GLUTHR4BB124 - 138136 - 150
217GLUTHR4CC124 - 138136 - 150
228GLUALA6AA139 - 147151 - 159
238GLUALA6BB139 - 147151 - 159
248GLUALA6CC139 - 147151 - 159
259VALGLY1AA151 - 220163 - 232
269VALGLY1BB151 - 220163 - 232
279VALGLY1CC151 - 220163 - 232
2810ARGSER5AA221 - 225233 - 237
2910ARGSER5BB221 - 225233 - 237
3010ARGSER5CC221 - 225233 - 237
3111ILEASP1AA226 - 254238 - 266
3211ILEASP1BB226 - 254238 - 266
3311ILEASP1CC226 - 254238 - 266
3412ARGILE1AA258 - 262270 - 274
3512ARGILE1BB258 - 262270 - 274
3612ARGILE1CC258 - 262270 - 274

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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

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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: 3.133836 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

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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

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Phasing

PhasingMethod: SAD

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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

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