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- PDB-5yf2: Crystal structure of CARNMT1 bound to anserine and SAH -

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Basic information

Entry
Database: PDB / ID: 5yf2
TitleCrystal structure of CARNMT1 bound to anserine and SAH
ComponentsCarnosine N-methyltransferase
KeywordsTRANSFERASE / SAM / methyltransferase
Function / homology
Function and homology information


carnosine N-methyltransferase / carnosine N-methyltransferase activity / carnosine metabolic process / Histidine catabolism / L-histidine catabolic process / S-adenosylmethionine-dependent methyltransferase activity / methylation / protein homodimerization activity / nucleus / cytosol
Similarity search - Function
Carnosine N-methyltransferase / Carnosine N-methyltransferase / N2227 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-8V3 / S-ADENOSYL-L-HOMOCYSTEINE / Carnosine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.802 Å
AuthorsCao, R. / Li, H.
CitationJournal: Cell Res. / Year: 2018
Title: Molecular basis for histidine N1 position-specific methylation by CARNMT1.
Authors: Cao, R. / Zhang, X. / Liu, X. / Li, Y. / Li, H.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carnosine N-methyltransferase
B: Carnosine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5209
Polymers84,9092
Non-polymers1,6127
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-33 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.690, 127.690, 320.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-695-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carnosine N-methyltransferase


Mass: 42454.281 Da / Num. of mol.: 2 / Fragment: methyltransferase domain (UNP RESIDUES 53-409)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARNMT1, C9orf41 / Plasmid: pHisGB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N4J0, carnosine N-methyltransferase

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-8V3 / (2~{S})-2-(3-azanylpropanoylamino)-3-(3-methylimidazol-4-yl)propanoic acid


Mass: 240.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 4.44 Å3/Da / Density % sol: 72.32 % / Mosaicity: 0.385 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 16% PEG8000, 0.1 M MES, pH 6.0, 0.2 M CaAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2017 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 38194 / % possible obs: 98 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.02 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.081 / Rrim(I) all: 0.165 / Χ2: 2.091 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.91.03618670.5380.5781.1911.58899.1
2.85-2.93.90.84219070.5760.4680.9671.55899.2
2.9-2.963.90.69218690.6860.3830.7941.53499.1
2.96-3.023.90.57718890.7250.3220.6631.56599.1
3.02-3.083.90.49218760.7880.2760.5671.59199
3.08-3.153.90.43819040.820.2450.5041.58999.1
3.15-3.233.80.36418780.8560.2030.4191.61898.8
3.23-3.323.90.28418910.9060.1580.3261.66698.8
3.32-3.423.90.23819060.9330.1330.2741.77598.8
3.42-3.533.90.19819000.9540.1110.2281.97998.8
3.53-3.653.80.15418870.9690.0860.1772.10398.6
3.65-3.83.80.14418940.970.0820.1672.1498.3
3.8-3.973.80.12819190.9780.0730.1482.45198.4
3.97-4.183.80.11118970.9830.0630.1282.56998.1
4.18-4.443.80.09219220.9860.0530.1072.8498.1
4.44-4.793.70.08519260.9880.0490.0992.96197.8
4.79-5.273.70.07619180.990.0430.0882.67597.3
5.27-6.033.60.08219220.9890.0480.0952.31395.8
6.03-7.593.80.0719750.9920.0410.0822.29997.1
7.59-503.50.05420470.9930.0330.0643.14392.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.388
Highest resolutionLowest resolution
Rotation45.25 Å2.98 Å

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→45.244 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1836 4.81 %random selection
Rwork0.1764 ---
obs0.1786 38191 98.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.07 Å2 / Biso mean: 53.9019 Å2 / Biso min: 22.85 Å2
Refinement stepCycle: final / Resolution: 2.802→45.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 107 189 5976
Biso mean--80.87 49.64 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085942
X-RAY DIFFRACTIONf_angle_d0.9678042
X-RAY DIFFRACTIONf_chiral_restr0.052847
X-RAY DIFFRACTIONf_plane_restr0.0051022
X-RAY DIFFRACTIONf_dihedral_angle_d16.9273530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8017-2.87750.31521290.25482727285698
2.8775-2.96210.30751260.24432774290099
2.9621-3.05770.27851320.23542775290799
3.0577-3.1670.3041310.23092778290999
3.167-3.29370.29591350.20862771290699
3.2937-3.44360.23791430.18462779292299
3.4436-3.62510.22881480.16462784293299
3.6251-3.85210.19581470.15532767291498
3.8521-4.14930.1721360.13862802293898
4.1493-4.56650.17691460.12842815296198
4.5665-5.22640.17681630.13162777294098
5.2264-6.58150.21531620.18682829299197
6.5815-45.25030.23561380.20342977311595
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.53250.4892-1.10930.6571-0.37481.1762-0.01820.17720.41520.10640.07530.0905-0.35660.0871-0.02020.4157-0.0806-0.01320.32130.09930.3802-42.922653.8815-3.1172
21.05220.4385-1.14740.7028-0.39992.5868-0.08810.0395-0.1063-0.03080.03250.00380.2232-0.09450.01750.31030.01860.02090.24340.12140.2969-51.387120.72720.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 58 through 409)A58 - 409
2X-RAY DIFFRACTION2(chain 'B' and resid 57 through 409)B57 - 409

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