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- PDB-4n8h: E61V mutant, RipA structure -

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Basic information

Entry
Database: PDB / ID: 4n8h
TitleE61V mutant, RipA structure
Components4-hydroxybutyrate coenzyme A transferase
KeywordsTRANSFERASE
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
4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)104,5092
Polymers104,5092
Non-polymers00
Water5,765320
1
A: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2541
Polymers52,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2541
Polymers52,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.907, 109.003, 85.014
Angle α, β, γ (deg.)90.00, 120.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-615-

HOH

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Components

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


Mass: 52254.371 Da / Num. of mol.: 2 / Mutation: E61V
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / pH: 5
Details: 0.3 M Na malonate, 22% PEG 3350, and 1 mM propionyl CoA, 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
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
ReflectionRedundancy: 3.7 % / Number: 136447 / Rmerge(I) obs: 0.061 / Χ2: 1.02 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 36693 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175099.710.0311.1583.7
4.15.1799.510.0431.0253.6
3.584.199.810.060.9643.6
3.263.5810010.0721.0093.7
3.023.2610010.0740.9753.7
2.853.0210010.0821.0433.7
2.72.8510010.0921.0263.8
2.592.710010.1210.9633.7
2.492.5910010.1311.0283.7
2.42.4910010.1591.0483.7
ReflectionResolution: 2.4→50 Å / Num. obs: 36693 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.24 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.159 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QLK

3qlk


Resolution: 2.4→39.7 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1986 5.47 %
Rwork0.151 --
obs0.154 36306 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 0 320 7116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046926
X-RAY DIFFRACTIONf_angle_d0.9019398
X-RAY DIFFRACTIONf_dihedral_angle_d13.0662576
X-RAY DIFFRACTIONf_chiral_restr0.0351076
X-RAY DIFFRACTIONf_plane_restr0.0041234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3984-2.45840.2311350.16312330X-RAY DIFFRACTION95
2.4584-2.52480.2331400.16452435X-RAY DIFFRACTION97
2.5248-2.59910.20891420.1662414X-RAY DIFFRACTION98
2.5991-2.6830.21661380.16952404X-RAY DIFFRACTION98
2.683-2.77890.23441420.172441X-RAY DIFFRACTION98
2.7789-2.89010.19761420.17382455X-RAY DIFFRACTION99
2.8901-3.02160.2191410.1722461X-RAY DIFFRACTION99
3.0216-3.18080.19981430.16892453X-RAY DIFFRACTION99
3.1808-3.380.22731440.16952471X-RAY DIFFRACTION100
3.38-3.64080.19941420.1572469X-RAY DIFFRACTION100
3.6408-4.00690.18471440.14622480X-RAY DIFFRACTION100
4.0069-4.5860.15641440.11882489X-RAY DIFFRACTION99
4.586-5.7750.17161430.12982499X-RAY DIFFRACTION100
5.775-39.70760.14971460.13972519X-RAY DIFFRACTION99
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)
11.54280.53750.08461.10080.12170.7247-0.09650.0806-0.0477-0.07450.0891-0.1605-0.02690.08480.00890.1694-0.02580.01440.1736-0.00650.1841-29.857329.7218-12.9533
20.0396-0.21670.10451.0058-0.66131.2083-0.00850.0363-0.1072-0.0944-0.0267-0.11830.1350.08790.02690.1713-0.00840.02110.1775-0.02960.2297-35.40856.0555-8.0795
31.617-0.6180.34440.9325-0.39950.9838-0.0342-0.04450.21420.1282-0.008-0.3034-0.08060.10510.0690.22520.0199-0.0210.2005-0.01860.2769-28.52691.587711.8335
40.9751-0.0487-0.0481.1179-0.14940.7192-0.0554-0.2958-0.09110.14630.10580.08030.00060.0566-0.03810.18580.04360.0110.2410.02920.1391-53.389410.889329.6799
51.83350.5993-0.27910.82450.14370.57380.0389-0.1026-0.03180.09170.0687-0.2279-0.07360.2619-0.06840.2425-0.0066-0.0180.2479-0.04590.2059-35.82126.747218.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 189 )
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 440 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 296 )
5X-RAY DIFFRACTION5chain 'B' and (resid 297 through 440 )

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