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- PDB-4n8j: F60M mutant, RipA structure -

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Basic information

Entry
Database: PDB / ID: 4n8j
TitleF60M mutant, RipA structure
ComponentsPutative 4-hydroxybutyrate coenzyme A transferase
KeywordsTRANSFERASE / Coenzyme A transferase
Function / homology
Function and homology information


acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function
Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
ACETATE ION / COENZYME A / PHOSPHATE ION / 4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsTorres, R. / Goulding, C.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase.
Authors: Torres, R. / Lan, B. / Latif, Y. / Chim, N. / Goulding, C.W.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Putative 4-hydroxybutyrate coenzyme A transferase
B: Putative 4-hydroxybutyrate coenzyme A transferase
C: Putative 4-hydroxybutyrate coenzyme A transferase
D: Putative 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,07923
Polymers209,0734
Non-polymers3,00619
Water24,3201350
1
A: Putative 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6125
Polymers52,2681
Non-polymers3444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6125
Polymers52,2681
Non-polymers3444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3215
Polymers52,2681
Non-polymers1,0524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5348
Polymers52,2681
Non-polymers1,2667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.307, 197.307, 59.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative 4-hydroxybutyrate coenzyme A transferase / Putative Coenzyme A transferase / Similar to 4-hydroxybutyrate CoA transferase


Mass: 52268.371 Da / Num. of mol.: 4 / Mutation: F60M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: aCH1, y2385, YPO1926, YP_1668 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZC36
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1350 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 3350, 0.4 M ammonium phosphate monobasic and 1 mM butyryl CoA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 173491 / % possible obs: 97.9 % / Redundancy: 5 % / Biso Wilson estimate: 27.61 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2-2.073.50.39614120179.5
2.07-2.1540.294176851100
2.15-2.254.60.226176511100
2.25-2.374.90.166177301100
2.37-2.5250.126177731100
2.52-2.715.10.098177051100
2.71-2.995.30.078176891100
2.99-3.425.50.072176991100
3.42-4.315.70.082177331100
4.31-505.70.05917706199.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.01→41.286 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9063 / SU ML: 0.16 / σ(F): 0.09 / Phase error: 16.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 1944 1.15 %
Rwork0.14 166617 -
obs0.1404 168561 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 257.64 Å2 / Biso mean: 44.1625 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: LAST / Resolution: 2.01→41.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13692 0 177 1350 15219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114115
X-RAY DIFFRACTIONf_angle_d1.28719160
X-RAY DIFFRACTIONf_chiral_restr0.0522168
X-RAY DIFFRACTIONf_plane_restr0.0072496
X-RAY DIFFRACTIONf_dihedral_angle_d13.7315257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0097-2.060.25371280.2022108321096088
2.06-2.11570.20961160.1755112031131992
2.1157-2.17790.21271370.1547115591169694
2.1779-2.24820.19571360.1503116481178495
2.2482-2.32850.17981290.1395118221195196
2.3285-2.42180.20891390.1419120081214798
2.4218-2.5320.17571430.1468120151215898
2.532-2.66540.18241440.1482121261227099
2.6654-2.83240.20041480.1491121761232499
2.8324-3.0510.17451480.15561219712345100
3.051-3.35790.19831440.14931227512419100
3.3579-3.84350.18461420.13381225412396100
3.8435-4.84130.13071480.10861226012408100
4.8413-41.2950.14011420.13361224212384100
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)
11.6821-0.0224-0.51351.50580.20841.2318-0.12-0.1986-0.13590.18080.05020.10030.06640.02330.05230.19140.06410.03540.26460.05420.135723.9476-44.549213.7328
20.72920.10540.31252.4778-0.06090.2979-0.00830.12710.0329-0.2596-0.02680.2528-0.0682-0.05610.04010.22580.0632-0.00460.2630.00290.16222.5654-35.2904-9.0556
34.1171-1.42880.45492.8771-0.40530.852-0.04-0.25310.0946-0.10640.04330.3205-0.0016-0.12710.02530.25660.0383-0.04030.24720.01610.230416.0546-14.5411-9.5288
40.1594-0.18680.39563.0774-1.64751.4715-0.14550.4113-0.17630.1839-0.07050.8567-0.3276-0.49590.30450.21520.0667-0.07990.4748-0.21620.461827.8812-57.9799-27.566
51.7385-0.0983-0.69771.86910.20512.3306-0.00440.4136-0.1989-0.3331-0.10830.0980.0533-0.10050.10210.23270.0875-0.02470.3351-0.08380.17450.8688-62.033-31.9624
64.6892-0.484-1.78573.44170.14312.9794-0.01810.0635-0.1870.02760.1237-0.37310.06040.2328-0.08460.17890.0776-0.01410.2915-0.08580.225462.1326-63.8653-27.4168
72.74030.1277-0.26851.5622-0.19870.47780.1260.2860.0093-0.1829-0.1605-0.1575-0.08890.06790.03820.25450.0619-0.00470.2876-0.00680.129657.1629-51.9931-26.8583
84.41360.721-0.73023.03980.4482.3622-0.00270.2151-0.0174-0.107-0.05290.19220.0116-0.13730.0510.16260.0514-0.01850.2256-0.04980.132140.2721-54.747-20.8629
92.3312-0.72110.79012.75541.15271.676-0.07720.0434-0.0802-0.0063-0.10850.25790.021-0.2030.17290.1820.02190.03080.3211-0.05930.212137.7743-58.1581-18.1409
105.93221.67263.70860.68150.91992.39310.3445-0.0114-0.88090.0973-0.0599-0.41240.1930.2124-0.29930.24880.0327-0.00530.36980.08380.363660.9218-64.5366-2.4089
112.07580.5925-0.18761.8444-0.2641.6540.0379-0.338-0.04890.2817-0.05350.0148-0.0020.1050.00780.15940.03870.00460.2817-0.0090.115351.9792-52.882-1.0302
121.87760.6792.77270.7880.42064.7173-0.13540.6812-0.0969-0.68430.23780.08120.02740.1271-0.10440.44120.0346-0.06890.4641-0.01560.446274.2619-53.911-14.49
133.8241-0.80220.47592.2756-0.17230.68240.1477-0.0338-0.2452-0.1225-0.151-0.26740.11420.06560.030.2050.0193-0.03380.28520.02730.23778.0135-50.3359-2.7883
141.728-0.4227-0.08671.6055-0.02160.83360.04170.11030.3587-0.1722-0.0741-0.1164-0.0527-0.01320.02490.2250.0362-0.02670.17490.06430.308935.47475.6308-12.0627
151.22050.5207-0.37231.396-0.57931.160.037-0.15330.25430.1705-0.0828-0.2034-0.1330.06460.06720.2280.0536-0.04720.2348-0.00540.332547.3464-5.36792.8588
162.307-0.057-1.01032.93170.34472.51150.0136-0.22620.29770.3982-0.08240.3004-0.2173-0.24380.09610.30460.07110.00520.3048-0.05510.211927.7896-13.815218.734
171.8642-0.17120.09891.37970.18850.9222-0.0055-0.21860.26910.0794-0.0273-0.2567-0.02270.05530.01990.1549-0.0076-0.06280.2413-0.00870.310485.7826-23.4218-0.2471
180.94160.35360.36981.70780.65551.1523-0.05760.12020.2944-0.22490.0052-0.1093-0.1310.06470.06950.18940.024-0.01820.27770.04580.336570.3403-18.639-15.1849
193.84370.1846-1.9262.69050.51713.5381-0.1970.00920.0255-0.15920.0868-0.35540.11370.4660.12840.19250.02090.00480.32650.02080.183772.081-35.9969-26.272
203.30571.6788-1.17762.8762-0.5572.9382-0.03620.5576-0.4038-0.4964-0.0903-0.56230.0670.16710.13210.3480.02660.09770.4609-0.01960.263573.6614-44.4261-36.8577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 189 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 346 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 347 through 440 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid -6 through 17 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 59 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 99 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 133 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 165 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 166 through 189 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 190 through 216 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 217 through 322 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 323 through 346 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 347 through 440 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 133 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 134 through 346 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 347 through 440 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 133 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 134 through 346 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 347 through 399 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 400 through 440 )D0

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