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- PDB-4jyc: MeaB, A Bacterial Homolog of MMAA, in its Apo form -

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Basic information

Entry
Database: PDB / ID: 4jyc
TitleMeaB, A Bacterial Homolog of MMAA, in its Apo form
ComponentsMethylmalonyl-CoA mutase accessory protein
KeywordsCHAPERONE / Alpha and beta protein / P-loop containing nucleoside triphosphate hydrolases / GTPase / Metallochaperone / Methylmalonyl-CoA Mutase (MCM)
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Methylmalonyl-CoA mutase accessory protein
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKoutmos, M. / Lofgren, M. / Padovani, D. / Banerjee, R.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: A switch III motif relays signaling between a B12 enzyme and its G-protein chaperone.
Authors: Lofgren, M. / Padovani, D. / Koutmos, M. / Banerjee, R.
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 accessory protein
D: Methylmalonyl-CoA mutase accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8335
Polymers142,3904
Non-polymers4431
Water7,260403
1
A: Methylmalonyl-CoA mutase accessory protein
D: Methylmalonyl-CoA mutase accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6383
Polymers71,1952
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-45 kcal/mol
Surface area26890 Å2
MethodPISA
2
B: Methylmalonyl-CoA mutase accessory protein
C: Methylmalonyl-CoA mutase accessory protein


Theoretical massNumber of molelcules
Total (without water)71,1952
Polymers71,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-38 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.463, 58.377, 155.280
Angle α, β, γ (deg.)90.00, 110.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Methylmalonyl-CoA mutase accessory protein


Mass: 35597.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: meaB, MexAM1_META1p0188 / Plasmid: pET-21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5AP93
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG400, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03262 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2009
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03262 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 79911 / Num. obs: 77430 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.086 / Net I/σ(I): 11.78
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.24 / Rsym value: 0.506 / % possible all: 93.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QM7

2qm7


Resolution: 2.2→48.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.814 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25217 3932 5.1 %RANDOM
Rwork0.19659 ---
obs0.19941 73498 96.96 %-
all-75802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.713 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-1.74 Å2
2--2.87 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9335 0 28 403 9766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199546
X-RAY DIFFRACTIONr_bond_other_d0.0010.029620
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.97112948
X-RAY DIFFRACTIONr_angle_other_deg0.78321798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89822.011368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.565151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26215111
X-RAY DIFFRACTIONr_chiral_restr0.0720.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022039
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 245 -
Rwork0.256 4868 -
obs--89.34 %

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