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- PDB-3e05: CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Ge... -

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Basic information

Entry
Database: PDB / ID: 300000
TitleCRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15
ComponentsPrecorrin-6Y C5,15-methyltransferase (Decarboxylating)
KeywordsTRANSFERASE / Porphyrin METABOLISM / S-ADENOSYL-METHIONINE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / METHYLTRANSFERASE / DECARBOXYLASE / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


protein methyltransferase activity / cobalamin biosynthetic process
Similarity search - Function
Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase / Precorrin-6Y methyltransferase / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase / Precorrin-6Y methyltransferase / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobalt-precorrin-6B C5,C15-methyltransferase and C12-decarboxylase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Ramagopal, U.A. / Toro, R. / Dickey, M. / Hu, S. / Maletic, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase from Geobacter metallireducens
Authors: Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Dickey, M. / Hu, S. / Maletic, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
B: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
C: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
D: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
E: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
F: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
G: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
H: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,33918
Polymers181,8718
Non-polymers46810
Water9,674537
1
A: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
D: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
E: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
G: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1709
Polymers90,9364
Non-polymers2345
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-108 kcal/mol
Surface area29850 Å2
MethodPISA
2
B: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
C: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
F: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
H: Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1709
Polymers90,9364
Non-polymers2345
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-111 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.710, 83.451, 149.056
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA215 - 3797 - 171
21PROPROLYSLYSBB215 - 3797 - 171
31PROPROLYSLYSCC215 - 3797 - 171
41PROPROLYSLYSDD215 - 3797 - 171
51PROPROLYSLYSEE215 - 3797 - 171
61PROPROLYSLYSFF215 - 3797 - 171
71PROPROLYSLYSGG215 - 3797 - 171
81LEULEULYSLYSHH211 - 3793 - 171
12LYSLYSTRPTRPAA387 - 401179 - 193
22LYSLYSTRPTRPBB387 - 401179 - 193
32LYSLYSTRPTRPCC387 - 401179 - 193
42LYSLYSTRPTRPDD387 - 401179 - 193
52LYSLYSTRPTRPEE387 - 401179 - 193
62LYSLYSTRPTRPFF387 - 401179 - 193
72LYSLYSTRPTRPGG387 - 401179 - 193
82LYSLYSTRPTRPHH387 - 401179 - 193

NCS ensembles :
ID
1
2

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Components

#1: Protein
Precorrin-6Y C5,15-methyltransferase (Decarboxylating)


Mass: 22733.916 Da / Num. of mol.: 8 / Fragment: C-terminal domain, residues 211-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / Gene: Gmet_0481 / Production host: Escherichia coli (E. coli)
References: UniProt: Q39YF0, precorrin-6B C5,15-methyltransferase (decarboxylating)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1800MM AMMONIUM TRI-CITRATE, PH 7.0, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 151124 / % possible obs: 92.3 % / Observed criterion σ(I): -5 / Redundancy: 3.6 % / Biso Wilson estimate: 32.206 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.5 / Rsym value: 0.91 / % possible all: 57.3

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.103 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26179 4038 3 %RANDOM
Rwork0.21572 ---
obs0.2171 130412 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.46 Å2
2--1.72 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11831 0 20 537 12388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.97416678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20251576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90524.674552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96152201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.21577
X-RAY DIFFRACTIONr_chiral_restr0.0870.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029165
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.35532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.58345
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.51307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.382
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.11527881
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.409312393
X-RAY DIFFRACTIONr_scbond_it4.8434950
X-RAY DIFFRACTIONr_scangle_it6.97354251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1155medium positional0.220.3
12B1155medium positional0.240.3
13C1155medium positional0.240.3
14D1155medium positional0.230.3
15E1155medium positional0.250.3
16F1155medium positional0.190.3
17G1155medium positional0.260.3
18H1155medium positional0.280.3
21A129medium positional0.190.3
22B129medium positional0.170.3
23C129medium positional0.190.3
24D129medium positional0.190.3
25E129medium positional0.80.3
26F129medium positional0.30.3
27G129medium positional0.190.3
28H129medium positional0.250.3
11A1155medium thermal1.542.5
12B1155medium thermal2.122.5
13C1155medium thermal2.392.5
14D1155medium thermal1.42.5
15E1155medium thermal1.452.5
16F1155medium thermal1.612.5
17G1155medium thermal1.482.5
18H1155medium thermal2.362.5
21A129medium thermal2.052.5
22B129medium thermal1.742.5
23C129medium thermal1.722.5
24D129medium thermal1.342.5
25E129medium thermal1.572.5
26F129medium thermal1.912.5
27G129medium thermal2.192.5
28H129medium thermal2.272.5
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 201 -
Rwork0.331 6967 -
obs--69.62 %

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