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- PDB-8dpb: MeaB in complex with the cobalamin-binding domain of its target m... -

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Basic information

Entry
Database: PDB / ID: 8dpb
TitleMeaB in complex with the cobalamin-binding domain of its target mutase with GMPPCP bound
Components(Methylmalonyl-CoA ...) x 2
KeywordsCHAPERONE / metalloenzyme maturation / complex / G-protein chaperone / cobalamin
Function / homology
Function and homology information


methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl-CoA mutase signature. / 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 ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl-CoA mutase signature. / 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Methylmalonyl-CoA mutase accessory protein / Methylmalonyl-CoA mutase, alpha subunit
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsVaccaro, F.A. / Born, D.A. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM131648 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008313 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery.
Authors: Vaccaro, F.A. / Born, D.A. / Drennan, C.L.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonyl-CoA mutase accessory protein
B: Methylmalonyl-CoA mutase accessory protein
C: Methylmalonyl-CoA mutase, alpha subunit
D: Methylmalonyl-CoA mutase, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,72610
Polymers109,4514
Non-polymers1,2756
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.230, 80.980, 166.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 12 or (resid 13...
d_2ens_1(chain "B" and (resid 5 through 12 or (resid 13...
d_1ens_2(chain "C" and (resid 564 through 566 or (resid 567...
d_2ens_2(chain "D" and (resid 564 or (resid 565 through 568...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUASPA2 - 16
d_12ens_1ALAVALA18 - 88
d_13ens_1PROLEUA90 - 100
d_14ens_1ASPPROA102 - 119
d_15ens_1PROSERA121 - 123
d_16ens_1THRTHRA125 - 136
d_17ens_1LEULEUA138 - 172
d_18ens_1LEUASPA174 - 179
d_19ens_1LEULYSA181 - 186
d_110ens_1ILEALAA188 - 200
d_111ens_1GLYTHRA203 - 224
d_112ens_1TRPLEUA230 - 259
d_113ens_1TRPARGA278 - 288
d_114ens_1THRARGA296 - 301
d_115ens_1HISLEUA308 - 320
d_21ens_1LEUASPG5 - 19
d_22ens_1ALAVALG21 - 91
d_23ens_1PROLEUG93 - 103
d_24ens_1ASPPROG105 - 122
d_25ens_1PROSERG124 - 126
d_26ens_1THRTHRG128 - 139
d_27ens_1LEULEUG141 - 175
d_28ens_1LEUASPG177 - 182
d_29ens_1LEULYSG184 - 189
d_210ens_1ILEALAG191 - 203
d_211ens_1GLYTHRG206 - 227
d_212ens_1TRPLEUG229 - 258
d_213ens_1TRPTRPG262
d_214ens_1ALAARGG265 - 274
d_215ens_1THRARGG285 - 290
d_216ens_1HISLEUG297 - 309
d_11ens_2PROLYSK2 - 28
d_12ens_2GLYPROK35 - 54
d_13ens_2PROASPK59 - 60
d_14ens_2ALASERK62 - 77
d_15ens_2GLYGLYK82 - 113
d_16ens_2GLYTHRK122 - 146
d_21ens_2PROLYSL2 - 28
d_22ens_2GLYGLYL30
d_23ens_2GLNPROL38 - 56
d_24ens_2PROASPL61 - 62
d_25ens_2ALASERL64 - 79
d_26ens_2GLYGLYL84 - 115
d_27ens_2GLYTHRL124 - 148

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.241822955965, 0.965393998462, -0.0976528837393), (0.94754944456, 0.21327425909, -0.238042308264), (-0.208977769351, -0.150095030376, -0.966333158788)-50.2006906681, 46.1896197442, 30.7918029435
2given(-0.198429532197, 0.978836297227, -0.0500522125713), (0.968849733298, 0.188172361623, -0.161001107479), (-0.14817528485, -0.0804404472408, -0.9856842392)-49.87080628, 44.2594454312, 32.9122347193

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Components

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Methylmalonyl-CoA ... , 2 types, 4 molecules ABCD

#1: Protein Methylmalonyl-CoA mutase accessory protein


Mass: 34492.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: meaB, MexAM1_META1p0188 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AP93
#2: Protein Methylmalonyl-CoA mutase, alpha subunit


Mass: 20232.949 Da / Num. of mol.: 2 / Fragment: cobalamin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: mcmA, MexAM1_META1p5251 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AV67, methylmalonyl-CoA mutase

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Non-polymers , 4 types, 73 molecules

#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.65 % / Description: thick plate-like crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: precipitant: 200 mM Lithium Chloride, 20% (w/v) PEG 3350; protein: 182 uM (20.2 mg/mL) complex in SEC buffer supplemented with 182 uM GMPPCP and 364 uM MgCl2); drop ratio: 150 nL of protein ...Details: precipitant: 200 mM Lithium Chloride, 20% (w/v) PEG 3350; protein: 182 uM (20.2 mg/mL) complex in SEC buffer supplemented with 182 uM GMPPCP and 364 uM MgCl2); drop ratio: 150 nL of protein to 230 nL of precipitant solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.72→48.99 Å / Num. obs: 24685 / % possible obs: 99.6 % / Redundancy: 8.4 % / Biso Wilson estimate: 49.55 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.158 / Net I/σ(I): 10.9
Reflection shellResolution: 2.72→2.84 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3897 / CC1/2: 0.804 / Rrim(I) all: 0.689 / % possible all: 99

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Processing

Software
NameVersionClassification
PHASERphasing
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.72→48.99 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 1178 4.78 %
Rwork0.2162 23448 -
obs0.2172 24626 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 2.72→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6501 0 78 67 6646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01166666
X-RAY DIFFRACTIONf_angle_d0.9069094
X-RAY DIFFRACTIONf_chiral_restr0.27421109
X-RAY DIFFRACTIONf_plane_restr0.00611186
X-RAY DIFFRACTIONf_dihedral_angle_d20.93772309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.97844058249
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.41521715604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.840.30291390.27992847X-RAY DIFFRACTION98.09
2.84-2.990.28721370.2632899X-RAY DIFFRACTION99.84
3-3.180.32151480.2392890X-RAY DIFFRACTION99.77
3.18-3.430.25321400.23672905X-RAY DIFFRACTION99.93
3.43-3.770.22821500.20772903X-RAY DIFFRACTION99.38
3.77-4.320.22551450.19492941X-RAY DIFFRACTION99.84
4.32-5.440.20771570.2022970X-RAY DIFFRACTION99.84
5.44-48.990.21311620.20353093X-RAY DIFFRACTION99.39

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