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- PDB-3hm2: Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 3hm2
TitleCrystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae
Componentsprecorrin-6Y C5,15-methyltransferase
KeywordsTRANSFERASE / alpha-beta-sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Methyltransferase
Function / homology
Function and homology information


protein methyltransferase activity / cobalamin biosynthetic process / methylation / metal ion binding
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 ...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
ACETIC ACID / Precorrin-6Y C5,15-methyltransferase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.205 Å
AuthorsKim, Y. / Bigelow, L. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae
Authors: Kim, Y. / Bigelow, L. / Keigher, L. / Joachimiak, A.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
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_leaving_atom_flag / _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 / _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: precorrin-6Y C5,15-methyltransferase
B: precorrin-6Y C5,15-methyltransferase
C: precorrin-6Y C5,15-methyltransferase
D: precorrin-6Y C5,15-methyltransferase
E: precorrin-6Y C5,15-methyltransferase
F: precorrin-6Y C5,15-methyltransferase
G: precorrin-6Y C5,15-methyltransferase
H: precorrin-6Y C5,15-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,83315
Polymers153,5248
Non-polymers3097
Water5,693316
1
A: precorrin-6Y C5,15-methyltransferase
B: precorrin-6Y C5,15-methyltransferase
C: precorrin-6Y C5,15-methyltransferase
D: precorrin-6Y C5,15-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9468
Polymers76,7624
Non-polymers1844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-41 kcal/mol
Surface area30970 Å2
MethodPISA
2
E: precorrin-6Y C5,15-methyltransferase
F: precorrin-6Y C5,15-methyltransferase
G: precorrin-6Y C5,15-methyltransferase
H: precorrin-6Y C5,15-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8867
Polymers76,7624
Non-polymers1243
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-36 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.782, 113.853, 84.650
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
precorrin-6Y C5,15-methyltransferase


Mass: 19190.488 Da / Num. of mol.: 8 / Fragment: residues 236-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC13129 / Gene: DIP1236 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q6NHA4
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate hydrate 20 %w/v Polyethylene glycol 3,350, pH ----, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→47.24 Å / Num. all: 72372 / Num. obs: 72372 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3635 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.205→47.238 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F / Details: twin_law=h,-k,-l
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3638 5.5 %random
Rwork0.21 ---
all0.213 66106 --
obs0.213 66106 88.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.84 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.303 Å20 Å2-6.0597 Å2
2--2.2797 Å20 Å2
3----0.6522 Å2
Refinement stepCycle: LAST / Resolution: 2.205→47.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10368 0 4 328 10700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.356
X-RAY DIFFRACTIONf_dihedral_angle_d21.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2047-2.24270.33411260.289826102736
2.2427-2.28350.34481380.292799
2.2835-2.32740.3651450.27992830
2.3274-2.37490.35831450.27112921
2.3749-2.42660.30581780.26062956
2.4266-2.4830.32081540.26312972
2.483-2.54510.331460.25672970
2.5451-2.61390.26791780.26123040
2.6139-2.69080.30251550.24943092
2.6908-2.77760.2961620.24063130
2.7776-2.87690.27941920.23793167
2.8769-2.99210.2831730.22993204
2.9921-3.12820.28591780.21613233
3.1282-3.29310.2311700.20163312
3.2931-3.49940.2751810.19423336
3.4994-3.76950.21611950.17573337
3.7695-4.14860.2282180.16943411
4.1486-4.74840.18791700.15093472
4.7484-5.98060.23731690.19213466
5.9806-47.24910.26581690.21643506

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