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- PDB-4ien: Crystal Structure of Acyl-CoA Hydrolase from Neisseria meningitid... -

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Basic information

Entry
Database: PDB / ID: 4ien
TitleCrystal Structure of Acyl-CoA Hydrolase from Neisseria meningitidis FAM18
ComponentsPutative acyl-CoA hydrolase
KeywordsHYDROLASE / Hot Dog Fold
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic 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
COENZYME A / GUANOSINE-5'-DIPHOSPHATE / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKhandokar, Y.B. / Forwood, J.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Expression, purification and crystallization of acetyl-CoA hydrolase from Neisseria meningitidis.
Authors: Khandokar, Y.B. / Londhe, A. / Patil, S. / Forwood, J.K.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acyl-CoA hydrolase
B: Putative acyl-CoA hydrolase
C: Putative acyl-CoA hydrolase
D: Putative acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08916
Polymers73,1044
Non-polymers4,98512
Water4,972276
1
A: Putative acyl-CoA hydrolase
B: Putative acyl-CoA hydrolase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)117,13324
Polymers109,6566
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area33670 Å2
ΔGint-225 kcal/mol
Surface area35500 Å2
MethodPISA
2
C: Putative acyl-CoA hydrolase
D: Putative acyl-CoA hydrolase
hetero molecules

C: Putative acyl-CoA hydrolase
D: Putative acyl-CoA hydrolase
hetero molecules

C: Putative acyl-CoA hydrolase
D: Putative acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,13324
Polymers109,6566
Non-polymers7,47718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area33410 Å2
ΔGint-229 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.520, 152.520, 152.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 5 - 158 / Label seq-ID: 8 - 161

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative acyl-CoA hydrolase


Mass: 18275.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: FAM18 / Gene: NMC1417 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3Plyse / References: UniProt: A1KUS8, acyl-CoA hydrolase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.04 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris pH8.5, 2M ammonium Phosphate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→35.95 Å / Num. all: 79721 / Num. obs: 79721 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.229 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
CCP4model building
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VPM

1vpm


Resolution: 2→35.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.939 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19449 3995 5 %RANDOM
Rwork0.16651 ---
obs0.16791 75650 99.97 %-
all-75673 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 308 276 5424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0195248
X-RAY DIFFRACTIONr_bond_other_d0.010.024908
X-RAY DIFFRACTIONr_angle_refined_deg2.592.0447148
X-RAY DIFFRACTIONr_angle_other_deg1.5983.00111296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92523.273220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97515888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9271544
X-RAY DIFFRACTIONr_chiral_restr0.1440.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215680
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021168
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88470.09
12B88470.09
21A88000.1
22C88000.1
31A87390.11
32D87390.11
41B88150.1
42C88150.1
51B87790.11
52D87790.11
61C87830.11
62D87830.11
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 297 -
Rwork0.205 5572 -
obs--100 %
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)
10.2386-0.0828-0.02630.42020.18910.2541-0.03650.01320.05990.01080.0353-0.0145-0.00490.04470.00120.02280.00150.00740.01090.00980.03246.5612-18.041629.9249
20.3726-0.0458-0.12240.26230.17670.4992-0.01810.09150.0308-0.021-0.00740.0403-0.0121-0.02570.02550.01950.00360.00660.02680.01450.019232.7176-28.02517.7296
30.28190.175-0.00190.2347-0.14020.4924-0.0017-0.07740.02290.022-0.0363-0.0207-0.0431-0.01120.0380.0337-0.00240.01470.0233-0.01320.027138.6252-24.1188-19.4245
40.27970.17880.01990.4826-0.21040.3877-0.0435-0.02920.059-0.03740.03810.0418-0.0186-0.0820.00540.03150.00570.01570.0201-0.00760.040625.9058-18.4816-35.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 158
2X-RAY DIFFRACTION2B5 - 158
3X-RAY DIFFRACTION3C5 - 158
4X-RAY DIFFRACTION4D5 - 158

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