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- PDB-1vpm: Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacill... -

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Basic information

Entry
Database: PDB / ID: 1vpm
TitleCrystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution
Componentsacyl-CoA hydrolase
KeywordsHYDROLASE / NP_241664.1 / 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 binding / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid metabolic process / cytosol
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
COENZYME A / PHOSPHATE ION / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Acyl-CoA hydrolase (NP_241664.1) from Bacillus halodurans at 1.66 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: acyl-CoA hydrolase
B: acyl-CoA hydrolase
C: acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7736
Polymers57,1433
Non-polymers1,6303
Water5,585310
1
A: acyl-CoA hydrolase
B: acyl-CoA hydrolase
C: acyl-CoA hydrolase
hetero molecules

A: acyl-CoA hydrolase
B: acyl-CoA hydrolase
C: acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,54712
Polymers114,2876
Non-polymers3,2606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area17850 Å2
ΔGint-107 kcal/mol
Surface area34850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.984, 106.507, 120.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11C-310-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA6 - 2018 - 32
21PROPROBB6 - 2018 - 32
31PROPROCC6 - 2018 - 32
42GLYGLYAA31 - 7143 - 83
52GLYGLYBB31 - 7143 - 83
62GLYGLYCC31 - 7143 - 83
73LYSLEUAA48 - 7660 - 88
83LYSLEUBB48 - 7660 - 88
93LYSLEUCC48 - 7660 - 88

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Components

#1: Protein acyl-CoA hydrolase


Mass: 19047.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH0798 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KEQ1, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.4 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.15M Na formate, 20.00% PEG 3350, 0.033M Cl2E9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979764,1.019943,0.979648
DetectorType: ADSC / Detector: CCD / Date: Oct 9, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797641
21.0199431
30.9796481
ReflectionResolution: 1.66→28.75 Å / Num. obs: 62701 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 33.53 Å2 / Rsym value: 0.099 / Net I/σ(I): 13
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 8969 / Rsym value: 0.553 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
SHELXSHARP/autoSHARPmodel building
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
SHELXphasing
SHARPphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66→28.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.078 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITIES FOR LOOPS 70-72 FOR CHAIN A, B AND C ARE AMBIGUOUS. 3. THE BIOLOGICAL UNIT IS LIKELY A HEXAMER WITH D3 SYMMETRY. WITHIN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITIES FOR LOOPS 70-72 FOR CHAIN A, B AND C ARE AMBIGUOUS. 3. THE BIOLOGICAL UNIT IS LIKELY A HEXAMER WITH D3 SYMMETRY. WITHIN THE HEXAMER, THERE ARE THREE DIMERS WITH A LARGE INTERACTION SURFACE. THESE DIMERS ARE FORMED FROM THE THREE MONOMERS IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT AND CRYSTALLOGRAPHIC SYMMETRY. THESE PAIRS ARE A:A' (8_565), B:C, AND B' (8_565):C' (8_565). THE COA BINDS AT THE INTERFACE BETWEEN THE DIMERS. FOR THE B:C DIMERS, ONLY ONE BINDING SITE IS OCCUPIED. A PHOSPHATE IS VISIBLE IN THE NON-CRYSTALLOGRAPHIC SYMMETRY COA BINDING SITE. THIS PHOSPHATE COULD BE FROM BUFFER OR PRODUCED BY HYDROLYSIS OF COA. THIS SECOND SITE IS PARTIALLY OCCLUDED BY THE PACKING OF HEXAMERS IN THE UNIT CELL. 4. THERE IS SOME EXTRA DENSITY NEAR CHAIN B/SER 10. IT WAS MODELED AS A CLOSE CONTACT WATER.
RfactorNum. reflection% reflectionSelection details
Rfree0.19669 3188 5.1 %RANDOM
Rwork0.17012 ---
obs0.17146 59512 99.36 %-
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: 26.825 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2---0.37 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.66→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 101 310 3892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223703
X-RAY DIFFRACTIONr_bond_other_d0.0010.023396
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9955061
X-RAY DIFFRACTIONr_angle_other_deg0.88737871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08523.581148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9241529
X-RAY DIFFRACTIONr_chiral_restr0.1020.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_nbd_refined0.2130.2699
X-RAY DIFFRACTIONr_nbd_other0.1920.23394
X-RAY DIFFRACTIONr_nbtor_other0.0850.22358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.222
X-RAY DIFFRACTIONr_mcbond_it2.63532493
X-RAY DIFFRACTIONr_mcbond_other0.6913933
X-RAY DIFFRACTIONr_mcangle_it3.27453799
X-RAY DIFFRACTIONr_scbond_it5.7981447
X-RAY DIFFRACTIONr_scangle_it7.504111262
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21813
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.070.21
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A476medium positional0.210.5
2B476medium positional0.130.5
3C476medium positional0.20.5
1A602loose positional0.575
2B602loose positional0.415
3C602loose positional0.465
1A476medium thermal1.042
2B476medium thermal1.272
3C476medium thermal1.182
1A602loose thermal2.3110
2B602loose thermal2.9110
3C602loose thermal2.410
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 222 4.95 %
Rwork0.255 4262 -
obs--97.04 %
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)
10.9746-0.1205-0.05960.6830.07950.95760.0052-0.0626-0.02020.0425-0.00160.0310.0982-0.0527-0.0036-0.1079-0.01240.007-0.0627-0.0083-0.0415-2.757957.912539.8724
20.8354-0.51830.77962.1313-1.35176.9206-0.0015-0.01550.0649-0.21010.0012-0.12520.20810.12540.0003-0.11850.00820.00730.024-0.0388-0.028337.543759.156440.7104
30.9125-0.46960.40981.608-0.25791.32230.06580.10220.03580.0056-0.0348-0.04860.09330.1306-0.031-0.13660.0293-0.01650.0153-0.0088-0.040618.524470.734444.6522
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 15614 - 168
22BB3 - 15315 - 165
33CC0 - 15312 - 165

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