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- PDB-4n8l: E249D mutant, RipA structure -

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Basic information

Entry
Database: PDB / ID: 4n8l
TitleE249D 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 / 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 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: 2.817 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,5412
Polymers104,5412
Non-polymers00
Water55831
1
A: Putative 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2701
Polymers52,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2701
Polymers52,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.241, 197.241, 59.223
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 52270.324 Da / Num. of mol.: 2 / Mutation: E249D
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.: 31 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis Tris, 27% PEG monomethyl ether 2000, and 1mM propionyl-CoA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.3 % / Number: 362778 / Rmerge(I) obs: 0.147 / Χ2: 1.09 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 32116 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.595099.710.0751.02310.7
6.037.5910010.1031.07911.2
5.276.0310010.1190.95911.3
4.795.2710010.1281.0811.4
4.444.7910010.1361.0711.3
4.184.4410010.1451.0811.4
3.974.1810010.151.06611.4
3.83.9710010.1631.09511.4
3.653.810010.181.03711.4
3.533.6510010.2051.04811.4
3.423.5310010.2221.0911.3
3.323.4210010.261.11711.3
3.233.3210010.2961.07411.3
3.153.2310010.3371.11311.3
3.083.1510010.3821.10911.3
3.023.0810010.4431.07911.3
2.963.0210010.511.12611.3
2.92.9610010.5831.1811.2
2.852.910010.6751.15611.3
2.82.8510010.8021.14811.2
ReflectionResolution: 2.8→50 Å / Num. obs: 32103 / % possible obs: 99.87 % / Redundancy: 11.3 % / Biso Wilson estimate: 66.59 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 18.02
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.851100
2.85-2.91100
2.9-2.961100
2.96-3.021100
3.02-3.081100
3.08-3.151100
3.15-3.231100
3.23-3.321100
3.32-3.421100
3.42-3.531100
3.53-3.651100
3.65-3.81100
3.8-3.971100
3.97-4.181100
4.18-4.441100
4.44-4.791100
4.79-5.271100
5.27-6.031100
6.03-7.591100
7.59-50199.7

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Processing

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

3qlk


Resolution: 2.817→42.704 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8458 / SU ML: 0.3 / Cross valid method: Free R / σ(F): 0 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1949 6.19 %Random
Rwork0.182 ---
obs0.1843 31507 98.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 281.04 Å2 / Biso mean: 87.0692 Å2 / Biso min: 33.87 Å2
Refinement stepCycle: LAST / Resolution: 2.817→42.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 0 31 6693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046786
X-RAY DIFFRACTIONf_angle_d0.9759206
X-RAY DIFFRACTIONf_chiral_restr0.0381056
X-RAY DIFFRACTIONf_plane_restr0.0041210
X-RAY DIFFRACTIONf_dihedral_angle_d13.3332528
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 (%)
2.817-2.88740.27671310.26581901203290
2.8874-2.96550.29911370.24492020215794
2.9655-3.05270.26341340.23582023215795
3.0527-3.15120.27271350.22692083221897
3.1512-3.26380.26061350.22272078221398
3.2638-3.39440.29111380.21092110224899
3.3944-3.54880.21411460.19922140228699
3.5488-3.73580.23761390.187921482287100
3.7358-3.96970.21911450.181921492294100
3.9697-4.2760.22561420.164721512293100
4.276-4.70580.18251410.151121362277100
4.7058-5.38560.21311410.156821862327100
5.3856-6.78090.18211390.181721832322100
6.7809-42.70880.19561460.167222502396100
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)
11.88750.73931.31922.01881.20052.2088-0.0669-0.44250.37010.3164-0.0735-0.0047-0.0594-0.08450.11360.4296-0.0891-0.01410.6304-0.16430.404949.5032-54.724529.28
22.5295-0.6823-0.51531.1555-0.49421.30660.02580.13920.4501-0.251-0.01380.0828-0.0632-0.0709-0.02280.3859-0.09760.0040.4688-0.04530.367353.3677-57.08014.6492
32.4037-0.2558-0.63441.9079-0.42211.1964-0.0346-0.13150.1820.0207-0.0623-0.6843-0.03310.42120.08370.4084-0.1074-0.00680.65540.03520.740775.1128-63.67937.6748
42.27890.27420.07731.8839-0.01520.696-0.07770.2658-0.307-0.1150.0044-0.34270.17920.15650.05720.46840.05320.20270.6072-0.02480.737782.0506-93.70913.5881
50.4998-0.6535-0.01551.66860.98491.1604-0.2841-0.1427-0.34810.56570.1921-1.0160.09790.4341-0.06140.78910.1672-0.08970.75070.11550.828577.933-94.741830.2351
61.5981-0.5009-0.5412.4022-0.38861.4852-0.1373-0.1356-0.24260.44760.0656-0.24370.0838-0.08040.01010.4848-0.01060.08640.55920.14640.591265.7626-97.248823.0364
71.34860.24960.40670.89790.76040.9077-0.29-0.37470.40680.74920.2207-0.98980.02590.1416-0.05590.80570.06-0.46210.8479-0.07421.001972.544-75.191731.526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 189 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 307 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 440 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 189 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 190 through 216 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 307 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 308 through 440 )B0

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