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- PDB-4xc8: Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg a... -

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Basic information

Entry
Database: PDB / ID: 4xc8
TitleIsobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg and without cobalamin (apo-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 ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Butyryl Coenzyme A / GUANOSINE-5'-DIPHOSPHATE / Fused isobutyryl-CoA mutase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 1.2Jan 27, 2016Group: Non-polymer description
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
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_seq_id / _struct_conn.ptnr2_label_asym_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)248,51410
Polymers245,8552
Non-polymers2,6598
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-115 kcal/mol
Surface area75770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)316.510, 316.510, 342.270
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 24:36 or resseq 54:66 or resseq 68:107 or resseq 109:112 or resseq 120:207)
211chain B and (resseq 24:36 or resseq 54:66 or resseq 68:107 or resseq 109:112 or resseq 120:207)
112(chain A and (resseq 209:216 or resseq 221:230 or resseq...
212(chain B and (resseq 209:216 or resseq 221:230 or resseq...
113chain A and (resseq 442:447 or resseq 449:477 or resseq...
213chain B and (resseq 442:447 or resseq 449:477 or resseq...
114chain A and (resseq 603:608 or resseq 620:621 or resseq...
214chain B and (resseq 603:608 or resseq 620:621 or resseq...
115chain A and (resseq 781:782 or resseq 784:808 or resseq...
215chain B and (resseq 781:782 or resseq 784:808 or resseq...

NCS ensembles :
ID
1
2
3
4
5

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Components

#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
#2: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 8.5
Details: precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5 protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL crystal soaked with 1 mM ...Details: precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5 protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL crystal soaked with 1 mM GDP and 1.5 mM MgCl2 for 6 hours

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→100 Å / Num. obs: 102338 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rsym value: 0.146 / Net I/σ(I): 11.3
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XC7

4xc7


Resolution: 3.25→99.159 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 5143 5.03 %retained from related apo-IcmF set
Rwork0.2054 ---
obs0.2063 102263 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→99.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16093 0 152 0 16245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216532
X-RAY DIFFRACTIONf_angle_d0.58222435
X-RAY DIFFRACTIONf_dihedral_angle_d11.2356005
X-RAY DIFFRACTIONf_chiral_restr0.0212511
X-RAY DIFFRACTIONf_plane_restr0.0032960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1168X-RAY DIFFRACTIONPOSITIONAL
12B1168X-RAY DIFFRACTIONPOSITIONAL0.009
21A1251X-RAY DIFFRACTIONPOSITIONAL
22B1251X-RAY DIFFRACTIONPOSITIONAL0.013
31A978X-RAY DIFFRACTIONPOSITIONAL
32B978X-RAY DIFFRACTIONPOSITIONAL0.041
41A1458X-RAY DIFFRACTIONPOSITIONAL
42B1458X-RAY DIFFRACTIONPOSITIONAL0.012
51A1463X-RAY DIFFRACTIONPOSITIONAL
52B1463X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.28690.42841650.40073221X-RAY DIFFRACTION99
3.2869-3.32560.34451740.36123234X-RAY DIFFRACTION99
3.3256-3.36610.35211780.32643197X-RAY DIFFRACTION99
3.3661-3.40880.2761800.30243178X-RAY DIFFRACTION99
3.4088-3.45360.28711500.28573183X-RAY DIFFRACTION98
3.4536-3.50090.33271550.2823200X-RAY DIFFRACTION98
3.5009-3.55090.28051690.27263206X-RAY DIFFRACTION100
3.5509-3.60390.26951660.26053267X-RAY DIFFRACTION100
3.6039-3.66030.26531660.25493256X-RAY DIFFRACTION100
3.6603-3.72030.27261830.24593224X-RAY DIFFRACTION100
3.7203-3.78440.23461640.24633253X-RAY DIFFRACTION100
3.7844-3.85320.25721700.22783253X-RAY DIFFRACTION100
3.8532-3.92740.23871780.22763211X-RAY DIFFRACTION100
3.9274-4.00750.22441610.21673275X-RAY DIFFRACTION100
4.0075-4.09470.22261660.21073226X-RAY DIFFRACTION100
4.0947-4.18990.18731740.19833216X-RAY DIFFRACTION100
4.1899-4.29470.22562070.18253214X-RAY DIFFRACTION99
4.2947-4.41080.19571610.18153227X-RAY DIFFRACTION99
4.4108-4.54060.18771670.16733171X-RAY DIFFRACTION98
4.5406-4.68720.18291800.17053234X-RAY DIFFRACTION99
4.6872-4.85470.20511680.1723251X-RAY DIFFRACTION100
4.8547-5.04910.18321720.1783260X-RAY DIFFRACTION100
5.0491-5.27880.20021720.1863262X-RAY DIFFRACTION100
5.2788-5.55710.26761590.20013275X-RAY DIFFRACTION100
5.5571-5.90530.23121850.21023245X-RAY DIFFRACTION100
5.9053-6.36110.22851720.21913271X-RAY DIFFRACTION99
6.3611-7.00110.19731870.18253159X-RAY DIFFRACTION97
7.0011-8.01380.20031690.17223298X-RAY DIFFRACTION100
8.0138-10.0950.16341840.14183315X-RAY DIFFRACTION100
10.095-99.20530.19111610.18333338X-RAY DIFFRACTION97
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)
14.07121.297-0.65920.375-0.34911.17250.1597-0.33510.33750.3323-0.10260.0832-0.1589-0.0429-0.05130.8717-0.03690.07860.9938-0.05950.9486-189.8844-83.103813.9383
21.21740.21070.44581.8733-0.58712.61790.0676-0.2878-0.12380.0203-0.0910.09410.3307-0.44880.01870.7623-0.2044-0.06780.96750.0590.4277-281.1163-108.883-39.2958
30.7358-1.67171.55510.0828-0.17821.1449-0.19020.54450.1019-0.1973-0.0097-0.25170.07850.4687-0.05970.4984-0.2735-0.14470.95870.30350.9335-208.4315-94.5244-21.3805
41.55530.15620.08730.8462-0.22871.17290.0575-0.24110.09760.2267-0.2174-0.133-0.3354-0.06660.14070.8269-0.1359-0.15970.78240.06930.47-252.1789-80.836-29.7982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:435 OR RESID 1102:1102 ) )A22 - 435
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:435 OR RESID 1102:1102 ) )A1102
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:435 OR RESID 1102:1102 ) )B22 - 435
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:435 OR RESID 1102:1102 ) )B1102
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 436:1093 OR RESID 1101:1101 ) )A436 - 1093
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 436:1093 OR RESID 1101:1101 ) )A1101
7X-RAY DIFFRACTION4( CHAIN B AND ( RESID 436:1093 OR RESID 1101:1101 ) )B436 - 1093
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 436:1093 OR RESID 1101:1101 ) )B1101

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