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- PDB-3ezx: Structure of Methanosarcina barkeri monomethylamine corrinoid protein -

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Basic information

Entry
Database: PDB / ID: 3ezx
TitleStructure of Methanosarcina barkeri monomethylamine corrinoid protein
ComponentsMonomethylamine corrinoid protein 1
KeywordsTRANSFERASE / N terminal all helical bundle C terminal Rossmann fold / Cobalt / Metal-binding / Methanogenesis
Function / homology
Function and homology information


monomethylamine methyltransferase activity / methanogenesis / cobalamin binding / cobalt ion binding
Similarity search - Function
Methyltransferase cognate corrinoid protein / Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain ...Methyltransferase cognate corrinoid protein / Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYBENZIMIDAZOLYLCOBAMIDE / Monomethylamine corrinoid protein 1
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.56 Å
AuthorsJain, R.
CitationJournal: TO BE PUBLISHED
Title: Structure of Methanosarcina barkeri monomethylamine corrinoid protein
Authors: Jain, R. / Hao, B. / Soares, J.A. / Zhang, L. / Green-Church, K. / Li, X. / Krzycki, J.A. / Chan, M.K.
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _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: Monomethylamine corrinoid protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3043
Polymers22,9621
Non-polymers1,3422
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Monomethylamine corrinoid protein 1
hetero molecules

A: Monomethylamine corrinoid protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6086
Polymers45,9252
Non-polymers2,6834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5790 Å2
ΔGint-51 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.970, 77.710, 100.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

21A-305-

HOH

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Components

#1: Protein Monomethylamine corrinoid protein 1 / MMCP 1


Mass: 22962.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / Strain: MS / References: UniProt: O30641
#2: Chemical ChemComp-HCB / 5-HYDROXYBENZIMIDAZOLYLCOBAMIDE


Mass: 1317.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60H84CoN13O15P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Magnesium acetate, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211.60296
SYNCHROTRONSSRL BL9-221.333117
SYNCHROTRONSSRL BL9-231.605839
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJan 1, 2004Double crystal monochromator
ADSC QUANTUM 42CCDJan 1, 2004Double crystal monochromator
ADSC QUANTUM 43CCDJan 1, 2004Double crystal monochromator
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2x-ray1
3x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.602961
21.3331171
31.6058391
ReflectionResolution: 2.56→50 Å / Num. all: 44512 / Num. obs: 15833 / % possible obs: 95.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 16.2
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.198 / % possible all: 75.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.56→45.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1915553.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1436 9.5 %RANDOM
Rwork0.205 ---
obs0.205 15144 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5886 Å2 / ksol: 0.351532 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-19.79 Å20 Å20 Å2
2---10.78 Å20 Å2
3----9.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.56→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 91 95 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d7.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.231.5
X-RAY DIFFRACTIONc_mcangle_it7.252
X-RAY DIFFRACTIONc_scbond_it8.542
X-RAY DIFFRACTIONc_scangle_it10.552.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.56→2.72 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 168 8.4 %
Rwork0.275 1825 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cob4.parcob4.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4mgh.parmgh.top

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