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- PDB-4xc7: Isobutyryl-CoA mutase fused with bound butyryl-CoA and without co... -

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Basic information

Entry
Database: PDB / ID: 4xc7
TitleIsobutyryl-CoA mutase fused with bound butyryl-CoA and without cobalamin or GDP (apo-IcmF)
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 / Cobalamin-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 / Cobalamin-binding domain / 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 / L(+)-TARTARIC ACID / Fused isobutyryl-CoA mutase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)247,8316
Polymers245,8552
Non-polymers1,9754
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-61 kcal/mol
Surface area77050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)318.180, 318.180, 344.710
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 27:36 or resseq 41:47 or resseq 49:107 or resseq 109:112 or resseq 121:206)
211chain B and (resseq 27:36 or resseq 41:47 or resseq 49:107 or resseq 109:112 or resseq 121:206)
112(chain A and (resseq 210:213 or resseq 217:229 or resseq...
212(chain B and (resseq 210:213 or resseq 217:229 or resseq...
113chain A and (resseq 442:447 or resseq 449:460 or resseq...
213chain B and (resseq 442:447 or resseq 449:460 or resseq...
114chain A and (resseq 603:607 or resseq 620:621 or resseq...
214chain B and (resseq 603:607 or resseq 620:621 or resseq...
115chain A and (resseq 776:779 or resseq 781:797 or resseq...
215chain B and (resseq 776:779 or resseq 781:797 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: sbm, 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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 + 1 uL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.45→100 Å / Num. obs: 84003 / % possible obs: 95.7 % / Redundancy: 10.4 % / Rsym value: 0.19 / Net I/σ(I): 11.7
Reflection shellResolution: 3.45→3.54 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 3.8 / % possible all: 55.4

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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: 4XC6

4xc6


Resolution: 3.45→91.851 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 4216 5.02 %retained from related holo-IcmF/GDP set
Rwork0.1864 ---
obs0.1873 83942 95.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→91.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16079 0 100 0 16179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216463
X-RAY DIFFRACTIONf_angle_d0.55722321
X-RAY DIFFRACTIONf_dihedral_angle_d10.2215971
X-RAY DIFFRACTIONf_chiral_restr0.0212501
X-RAY DIFFRACTIONf_plane_restr0.0032958
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1236X-RAY DIFFRACTIONPOSITIONAL
12B1236X-RAY DIFFRACTIONPOSITIONAL0.01
21A1140X-RAY DIFFRACTIONPOSITIONAL
22B1140X-RAY DIFFRACTIONPOSITIONAL0.013
31A925X-RAY DIFFRACTIONPOSITIONAL
32B925X-RAY DIFFRACTIONPOSITIONAL0.007
41A1385X-RAY DIFFRACTIONPOSITIONAL
42B1385X-RAY DIFFRACTIONPOSITIONAL0.009
51A1494X-RAY DIFFRACTIONPOSITIONAL
52B1494X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.48920.3026660.24951392X-RAY DIFFRACTION50
3.4892-3.53030.2478640.27491623X-RAY DIFFRACTION59
3.5303-3.57330.29711060.27271938X-RAY DIFFRACTION70
3.5733-3.61860.34141340.27362559X-RAY DIFFRACTION92
3.6186-3.66620.26521420.26172773X-RAY DIFFRACTION100
3.6662-3.71640.25681410.25962736X-RAY DIFFRACTION100
3.7164-3.76950.26941550.24992738X-RAY DIFFRACTION100
3.7695-3.82580.22611350.24312766X-RAY DIFFRACTION100
3.8258-3.88550.27931540.2342751X-RAY DIFFRACTION100
3.8855-3.94920.26211510.22772750X-RAY DIFFRACTION100
3.9492-4.01730.23691390.2172794X-RAY DIFFRACTION100
4.0173-4.09040.25181520.21542778X-RAY DIFFRACTION100
4.0904-4.16910.20281390.19992731X-RAY DIFFRACTION100
4.1691-4.25420.17041530.18172760X-RAY DIFFRACTION100
4.2542-4.34670.22011680.17352753X-RAY DIFFRACTION100
4.3467-4.44780.18051340.16572757X-RAY DIFFRACTION100
4.4478-4.5590.18211490.15262763X-RAY DIFFRACTION100
4.559-4.68230.13781550.15722778X-RAY DIFFRACTION100
4.6823-4.820.17721560.15442770X-RAY DIFFRACTION100
4.82-4.97560.17531380.15782771X-RAY DIFFRACTION100
4.9756-5.15340.17251470.172797X-RAY DIFFRACTION100
5.1534-5.35970.2251340.18842761X-RAY DIFFRACTION100
5.3597-5.60360.23151460.19232789X-RAY DIFFRACTION100
5.6036-5.8990.22911590.19992780X-RAY DIFFRACTION100
5.899-6.26850.21261540.20492790X-RAY DIFFRACTION100
6.2685-6.75240.20221560.18552786X-RAY DIFFRACTION100
6.7524-7.43160.20671490.17112795X-RAY DIFFRACTION100
7.4316-8.50640.15231480.14312814X-RAY DIFFRACTION100
8.5064-10.71450.14661510.12582823X-RAY DIFFRACTION100
10.7145-91.88320.20121410.19642910X-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)
11.35870.04930.82130.2892-0.03680.5062-0.06760.3310.1699-0.05090.0664-0.0338-0.0590.15420.01130.6196-0.12430.0181.0557-0.01340.8527-202.9047-90.8035-8.5454
20.99410.30240.22290.9039-0.1111.22720.0428-0.15330.02360.0889-0.0525-0.0268-0.2133-0.1420.01030.7278-0.0411-0.06630.72550.07130.4957-264.7698-92.087-33.6266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:1093 OR RESID 1101:1101 ) )A22 - 1093
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:1093 OR RESID 1101:1101 ) )A1101
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1101 ) )B22 - 1093
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1101 ) )B1101

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