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- PDB-4xc6: Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, an... -

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Basic information

Entry
Database: PDB / ID: 4xc6
TitleIsobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, and Mg (holo-IcmF/GDP)
ComponentsIsobutyryl-CoA mutase fused
KeywordsISOMERASE / Radical enzyme / complex / G-protein chaperone
Function / homology
Function and homology information


isobutyryl-CoA mutase / pivalyl-CoA mutase activity / isobutyryl-CoA mutase activity / methylmalonyl-CoA mutase activity / acyl-CoA metabolic process / cobalamin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / magnesium ion binding
Similarity search - Function
Fused isobutyryl-CoA mutase / Methylmalonyl Co-A mutase-associated GTPase MeaB / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. ...Fused isobutyryl-CoA mutase / Methylmalonyl Co-A mutase-associated GTPase MeaB / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-DEOXYADENOSINE / ACETATE ION / COBALAMIN / GUANOSINE-5'-DIPHOSPHATE / Fused isobutyryl-CoA mutase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.35 Å
AuthorsJost, M. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Visualization of a radical B12 enzyme with its G-protein chaperone.
Authors: Jost, M. / Cracan, V. / Hubbard, P.A. / Banerjee, R. / Drennan, C.L.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isobutyryl-CoA mutase fused
B: Isobutyryl-CoA mutase fused
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,81012
Polymers245,8552
Non-polymers3,95510
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-133 kcal/mol
Surface area74680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)318.760, 318.760, 343.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 23:37 or resseq 41:47 or resseq 49:133 or resseq 135:145 or resseq 147:207)
211chain B and (resseq 23:38 or resseq 40:47 or resseq 49:133 or resseq 135:145 or resseq 147:207)
112(chain A and (resseq 209:230 or resseq 232:250 or resseq...
212(chain B and (resseq 209:230 or resseq 232:250 or resseq...
113chain A and (resseq 442:487 or resseq 493:528 or resseq...
213chain B and (resseq 442:487 or resseq 493:528 or resseq...
114chain A and (resseq 602:608 or resseq 621:637 or resseq...
214chain B and (resseq 602:608 or resseq 621:637 or resseq...
115chain A and (resseq 781:782 or resseq 784:805 or resseq...
215chain B and (resseq 781:782 or resseq 784:805 or resseq...

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isobutyryl-CoA mutase fused


Mass: 122927.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: IcmF is misannotated as sbm in the genome of Cupriavidus metallidurans.
Source: (gene. exp.) Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) (bacteria)
Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: IcmF, Rmet_0210 / Plasmid: pET28a
Details (production host): gene inserted at NdeI and BamHI sites, N-terminal hexahistidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1LRY0, isobutyryl-CoA mutase

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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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: 6.7 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: precipitant: 700 mM potassium sodium tartrate, 200 mM ammonium acetate, 100 mM imidazole pH 7. 3% (v/v) ethylene glycol additive in drop solution only. protein in 100 mM NaCl, 50 mM HEPES pH ...Details: precipitant: 700 mM potassium sodium tartrate, 200 mM ammonium acetate, 100 mM imidazole pH 7. 3% (v/v) ethylene glycol additive in drop solution only. protein in 100 mM NaCl, 50 mM HEPES pH 7.5, 1 mM GDP, 3 mM MgCl2, 0.3 mM adenosylcobalamin, mixed with precipitant 1uL + 1uL set up under red light, grown in the dark

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 94999 / % possible obs: 99.2 % / Redundancy: 9.3 % / Rsym value: 0.129 / Net I/σ(I): 15.1
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
Cootmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 3.35→48.69 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 4764 5.02 %Random selection
Rwork0.1801 ---
obs0.181 94948 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16282 0 264 0 16546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316853
X-RAY DIFFRACTIONf_angle_d0.61622869
X-RAY DIFFRACTIONf_dihedral_angle_d11.1576233
X-RAY DIFFRACTIONf_chiral_restr0.0242546
X-RAY DIFFRACTIONf_plane_restr0.0033083
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1323X-RAY DIFFRACTIONPOSITIONAL
12B1323X-RAY DIFFRACTIONPOSITIONAL0.01
21A1375X-RAY DIFFRACTIONPOSITIONAL
22B1375X-RAY DIFFRACTIONPOSITIONAL0.014
31A1026X-RAY DIFFRACTIONPOSITIONAL
32B1026X-RAY DIFFRACTIONPOSITIONAL0.04
41A1393X-RAY DIFFRACTIONPOSITIONAL
42B1393X-RAY DIFFRACTIONPOSITIONAL0.016
51A1460X-RAY DIFFRACTIONPOSITIONAL
52B1460X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.38810.31271590.30412955X-RAY DIFFRACTION98
3.3881-3.4280.31281420.28422972X-RAY DIFFRACTION98
3.428-3.46980.27131430.27132931X-RAY DIFFRACTION97
3.4698-3.51370.28091580.262941X-RAY DIFFRACTION98
3.5137-3.55990.23221400.24712962X-RAY DIFFRACTION98
3.5599-3.60860.27431590.2492960X-RAY DIFFRACTION98
3.6086-3.66020.27881500.24542953X-RAY DIFFRACTION98
3.6602-3.71480.29171550.25132907X-RAY DIFFRACTION97
3.7148-3.77280.21761640.22622928X-RAY DIFFRACTION97
3.7728-3.83460.22921460.21762973X-RAY DIFFRACTION99
3.8346-3.90070.25581770.22933003X-RAY DIFFRACTION100
3.9007-3.97160.28731480.22213043X-RAY DIFFRACTION100
3.9716-4.0480.22341490.19333002X-RAY DIFFRACTION100
4.048-4.13060.19221650.17763007X-RAY DIFFRACTION100
4.1306-4.22030.17331590.16873028X-RAY DIFFRACTION100
4.2203-4.31850.17551890.15672996X-RAY DIFFRACTION100
4.3185-4.42640.17461500.14683055X-RAY DIFFRACTION100
4.4264-4.5460.16121640.1452985X-RAY DIFFRACTION100
4.546-4.67960.15371650.14273031X-RAY DIFFRACTION100
4.6796-4.83060.16961680.14513020X-RAY DIFFRACTION100
4.8306-5.0030.18711540.15243038X-RAY DIFFRACTION100
5.003-5.20310.18521520.16223039X-RAY DIFFRACTION100
5.2031-5.43960.17661490.17353062X-RAY DIFFRACTION100
5.4396-5.7260.20151680.17423019X-RAY DIFFRACTION100
5.726-6.08410.23011700.1843028X-RAY DIFFRACTION100
6.0841-6.55290.21571710.18373039X-RAY DIFFRACTION100
6.5529-7.21040.16081660.16153046X-RAY DIFFRACTION100
7.2104-8.24940.15641570.1413075X-RAY DIFFRACTION100
8.2494-10.37680.11911730.11873076X-RAY DIFFRACTION100
10.3768-48.69530.1871540.16913110X-RAY DIFFRACTION98
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)
11.5387-0.08520.56410.4568-0.12880.8735-0.0222-0.1785-0.0165-0.05420.0397-0.2368-0.0118-0.0243-0.00890.4474-0.0270.05350.53550.0430.7868-203.6495-91.0849-10.4717
20.97020.38980.16820.83040.10190.88380.0401-0.09310.0520.02-0.0963-0.02330.0907-0.2290.05620.7143-0.0404-0.02430.660.0690.4141-265.0706-93.229-33.6325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )A21 - 1093
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )A1101 - 1102
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )A1103
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1101 OR RESID 1102:1102 ) )B22 - 1093
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1101 OR RESID 1102:1102 ) )B1101
6X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1101 OR RESID 1102:1102 ) )B1102

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