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- PDB-4n8i: M31G mutant, RipA structure -

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Basic information

Entry
Database: PDB / ID: 4n8i
TitleM31G mutant, RipA structure
Components4-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
ACETATE ION / COENZYME A / 4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 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 ...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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0746
Polymers104,4202
Non-polymers1,6534
Water10,647591
1
A: 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0373
Polymers52,2101
Non-polymers8272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0373
Polymers52,2101
Non-polymers8272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint5 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.411, 107.171, 87.800
Angle α, β, γ (deg.)90.00, 120.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 52210.207 Da / Num. of mol.: 2 / Mutation: M31G
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-COA / COENZYME A / Coenzyme A


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 46.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M ammonium acetate, 24% PEG 3350 and 1 mM succinyl-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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 61943 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.01-2.082.70.293196.5
2.08-2.173.10.244199.7
2.17-2.263.70.2081100
2.26-2.383.80.1691100
2.38-2.533.80.1361100
2.53-2.733.80.1091100
2.73-33.80.0851100
3-3.443.80.0771100
3.44-4.333.80.0811100
4.33-503.70.0551100

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Processing

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

3qlk


Resolution: 2.011→43.748 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.19 / Cross valid method: Free R / σ(F): 0 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 1913 3.21 %Random
Rwork0.1351 ---
obs0.1366 59636 95.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4998 Å2
Refinement stepCycle: LAST / Resolution: 2.011→43.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6792 0 102 591 7485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127063
X-RAY DIFFRACTIONf_angle_d1.4029600
X-RAY DIFFRACTIONf_dihedral_angle_d14.4172642
X-RAY DIFFRACTIONf_chiral_restr0.0691085
X-RAY DIFFRACTIONf_plane_restr0.0071251
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 (%)
2.0112-2.06150.27181160.19653593370984
2.0615-2.11730.19391280.16483840396890
2.1173-2.17960.16641320.153985411792
2.1796-2.24990.2311350.14284052418795
2.2499-2.33030.18631330.13424080421395
2.3303-2.42360.18251280.1314108423696
2.4236-2.53390.17281420.13314153429597
2.5339-2.66750.16781420.13844233437598
2.6675-2.83460.1861410.13794207434898
2.8346-3.05340.21121420.13564221436399
3.0534-3.36060.19791440.13634284442899
3.3606-3.84660.15311420.126542724414100
3.8466-4.84530.14161440.108443264470100
4.8453-43.75850.18711440.14543694513100
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)
10.64780.3857-0.10321.2547-0.2380.7947-0.0670.00260.0125-0.12110.044-0.23810.05610.06360.01710.1739-0.03790.02950.1826-0.0090.2196-23.696328.6097-13.5908
20.21080.130.04830.824-0.31860.6856-0.05240.0288-0.0327-0.10070.0398-0.10190.03530.08580.01580.1562-0.01270.0230.1784-0.01610.1879-35.14310.9198-9.985
30.873-0.1322-0.01561.0254-0.3790.9161-0.0351-0.1203-0.0330.0612-0.0283-0.1946-0.04790.19660.0160.14430.0207-0.00410.18620.0110.2241-26.5362-2.184812.725
40.96930.0012-0.09320.5327-0.11420.83870.029-0.1612-0.3182-0.02560.03640.1950.3168-0.09370.01290.31250.00430.02520.22920.08520.2758-64.0469-10.721834.3845
50.651-0.0112-0.32921.1658-0.17371.1045-0.0533-0.2334-0.13830.2473-0.0393-0.18620.08980.28180.03090.28050.0498-0.040.29140.06170.2094-42.8944-2.650335.6713
61.0291-0.0232-0.59360.6545-0.20860.943-0.0946-0.1289-0.1340.08420.0577-0.03620.09990.07580.01910.21080.0295-0.00970.18460.01970.1745-52.5228-0.637325.3288
70.57870.29130.21021.1014-0.36820.897-0.0682-0.1158-0.07110.11820.09980.09470.0242-0.18750.02340.22020.04210.03630.22140.0280.2071-64.75972.099630.3085
80.4790.24-0.22290.1459-0.08590.29170.1287-0.25630.10910.3229-0.0136-0.0581-0.19290.251-0.00040.3347-0.0243-0.02370.3042-0.08350.2448-45.629623.502932.8107
90.8787-0.0777-0.18391.37120.27660.9958-0.0617-0.15310.290.2322-0.0096-0.139-0.21350.090.01040.25270.0197-0.0350.1661-0.03310.222-52.098926.059524.1767
101.0475-0.1613-0.16550.96060.00431.0454-0.0951-0.15140.09920.18740.04580.0679-0.1838-0.06560.00330.22530.0434-0.00340.1799-0.01720.1971-60.478419.894724.8848
110.83010.2768-0.45450.6178-0.07820.51770.0042-0.1233-0.03630.1188-0.0176-0.0837-0.0430.1097-0.0030.20450.0068-0.01810.19270.00040.1604-43.199915.956218.242
121.21010.2666-0.09140.8070.14840.95080.0243-0.20440.0080.1976-0.0494-0.1366-0.0540.17640.00930.2335-0.0246-0.03020.21860.00970.1935-35.123520.675618.1524
130.67580.2017-0.10780.62110.38221.51450.0244-0.17080.14950.0445-0.0382-0.097-0.13950.3393-0.00790.2343-0.0708-0.05230.2908-0.01850.2741-23.774128.663115.8376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 99 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 357 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 440 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 25 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 99 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 165 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 166 through 189 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 190 through 216 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 217 through 260 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 261 through 296 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 297 through 342 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 343 through 399 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 400 through 440 )B0

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