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- PDB-5cjt: Isobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, Mg... -

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Basic information

Entry
Database: PDB / ID: 5cjt
TitleIsobutyryl-CoA mutase fused with bound adenosylcobalamin, GDP, Mg (holo-IcmF/GDP), and substrate isobutyryl-coenzyme A
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 / COBALAMIN / ISOBUTYRYL-COENZYME A / GUANOSINE-5'-DIPHOSPHATE / Fused isobutyryl-CoA mutase
Similarity search - Component
Biological speciesRalstonia metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.
Authors: Jost, M. / Born, D.A. / Cracan, V. / Banerjee, R. / Drennan, C.L.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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.pdbx_ptnr2_label_alt_id / _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)251,42613
Polymers245,8552
Non-polymers5,57111
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-124 kcal/mol
Surface area73040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)316.840, 316.840, 342.650
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 49:145 or resseq 147:207)
211chain B and (resseq 23:37 or resseq 41:47 or resseq 49:145 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 442:447 or resseq 449:477 or resseq...
213chain B and (resseq 442:447 or resseq 449:477 or resseq...
114chain A and (resseq 602:608 or resseq 621:639 or resseq...
214chain B and (resseq 602:608 or resseq 621:639 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

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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 misannoated as sbm in the C. metallidurans genome
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, methylmalonyl-CoA mutase

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Non-polymers , 5 types, 11 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-CO6 / ISOBUTYRYL-COENZYME A / IB-CO6 / Isobutyryl-CoA


Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S / Comment: antibiotic*YM
#5: 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
#6: 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

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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 7.7. 3% (v/v) ethylene glycol additive in drop solution only. protein in 100 mM NaCl, 50 mM HEPES ...Details: precipitant: 700 mM potassium sodium tartrate, 200 mM ammonium acetate, 100 mM imidazole pH 7.7. 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 1 uL + 1 uL set up under red light, grown in the dark, soaked with 5 mM isobutyryl-coenzyme A for 30 s

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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: 3.4→35 Å / Num. obs: 87533 / % possible obs: 96.9 % / Redundancy: 4.3 % / Rsym value: 0.126 / Net I/σ(I): 10.6
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XC6

4xc6


Resolution: 3.4→34.824 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 4398 5.03 %copied from entry 4XC6
Rwork0.1893 ---
obs0.1903 87444 96.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→34.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16176 0 340 0 16516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316845
X-RAY DIFFRACTIONf_angle_d0.59222881
X-RAY DIFFRACTIONf_dihedral_angle_d10.8826240
X-RAY DIFFRACTIONf_chiral_restr0.0232554
X-RAY DIFFRACTIONf_plane_restr0.0033108
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1326X-RAY DIFFRACTIONPOSITIONAL
12B1326X-RAY DIFFRACTIONPOSITIONAL0.009
21A1388X-RAY DIFFRACTIONPOSITIONAL
22B1388X-RAY DIFFRACTIONPOSITIONAL0.012
31A1009X-RAY DIFFRACTIONPOSITIONAL
32B1009X-RAY DIFFRACTIONPOSITIONAL0.041
41A1435X-RAY DIFFRACTIONPOSITIONAL
42B1435X-RAY DIFFRACTIONPOSITIONAL0.015
51A1507X-RAY DIFFRACTIONPOSITIONAL
52B1507X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.34171370.34392795X-RAY DIFFRACTION99
3.4386-3.4790.35861500.34212860X-RAY DIFFRACTION99
3.479-3.52140.32731320.31972780X-RAY DIFFRACTION99
3.5214-3.56590.29641530.29582798X-RAY DIFFRACTION99
3.5659-3.61280.31641410.28592813X-RAY DIFFRACTION99
3.6128-3.66220.32211470.27262788X-RAY DIFFRACTION98
3.6622-3.71450.2771510.24812815X-RAY DIFFRACTION99
3.7145-3.76990.24081470.24382777X-RAY DIFFRACTION98
3.7699-3.82870.25761400.2412779X-RAY DIFFRACTION98
3.8287-3.89140.27571620.23712783X-RAY DIFFRACTION98
3.8914-3.95840.26451460.22822798X-RAY DIFFRACTION98
3.9584-4.03030.24471360.22182792X-RAY DIFFRACTION98
4.0303-4.10770.20751460.19532790X-RAY DIFFRACTION98
4.1077-4.19140.18471530.18762772X-RAY DIFFRACTION98
4.1914-4.28240.20481730.16822773X-RAY DIFFRACTION98
4.2824-4.38180.15961450.15822780X-RAY DIFFRACTION98
4.3818-4.49120.17691520.15172781X-RAY DIFFRACTION97
4.4912-4.61240.16431420.15632785X-RAY DIFFRACTION97
4.6124-4.74780.18911600.1592736X-RAY DIFFRACTION97
4.7478-4.90060.18831430.16222789X-RAY DIFFRACTION97
4.9006-5.07520.20631420.16782753X-RAY DIFFRACTION97
5.0752-5.27780.19531420.17432769X-RAY DIFFRACTION96
5.2778-5.51710.21031320.1832772X-RAY DIFFRACTION96
5.5171-5.80670.22231480.18912735X-RAY DIFFRACTION96
5.8067-6.16860.21791540.19492752X-RAY DIFFRACTION96
6.1686-6.64190.1921570.18512721X-RAY DIFFRACTION95
6.6419-7.30470.19691440.16762706X-RAY DIFFRACTION94
7.3047-8.3490.16951360.14372721X-RAY DIFFRACTION93
8.349-10.47120.11951490.122678X-RAY DIFFRACTION92
10.4712-34.82550.20611380.17082655X-RAY DIFFRACTION89
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)
11.5566-0.0260.51120.5543-0.07380.8848-0.0154-0.1656-0.0269-0.04860.018-0.2596-0.0074-0.01360.00390.4731-0.02640.06250.54410.04880.7646-202.48-90.6115-10.5344
21.01130.35440.14020.75940.01380.7970.0205-0.08680.05420.009-0.0875-0.00560.0622-0.22230.0660.8246-0.0301-0.00770.76390.05190.5107-263.388-92.5861-33.5861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1103 OR RESID 1104:1104 ) )A21 - 1093
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1103 OR RESID 1104:1104 ) )A1101 - 1103
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:1093 OR RESID 1101:1103 OR RESID 1104:1104 ) )A1104
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )B22 - 1093
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )B1101 - 1102
6X-RAY DIFFRACTION2( CHAIN B AND ( RESID 22:1093 OR RESID 1101:1102 OR RESID 1103:1103 ) )B1103

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