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- PDB-5yf1: Crystal structure of CARNMT1 bound to carnosine and SFG -

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Basic information

Entry
Database: PDB / ID: 5yf1
TitleCrystal structure of CARNMT1 bound to carnosine and SFG
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-8V0 / ACETATE ION / SINEFUNGIN / Carnosine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.399 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_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)86,50813
Polymers84,9092
Non-polymers1,60011
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-7 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.125, 128.125, 324.643
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-503-

CA

21B-733-

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 , 6 types, 372 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-8V0 / (2~{S})-2-(3-azanylpropanoylamino)-3-(1~{H}-imidazol-4-yl)propanoic acid / Carnosine


Mass: 226.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 361 / 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: 4.53 Å3/Da / Density % sol: 72.85 % / Mosaicity: 0.401 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 16% PEG 8000, 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 16, 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: 2.399→50 Å / Num. obs: 62119 / % possible obs: 97.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 35.99 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.069 / Rrim(I) all: 0.146 / Χ2: 1.81 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.10.84530460.5950.4640.9681.40899.4
2.44-2.494.20.80230470.6480.4390.9181.45899.7
2.49-2.534.20.68630360.7090.3730.7841.40699.6
2.53-2.594.20.65830660.7220.3580.7521.48199.5
2.59-2.644.20.52130480.7880.2810.5941.45999.5
2.64-2.74.20.47330580.8190.2550.5391.50699.4
2.7-2.774.20.40830580.870.2190.4651.46799.4
2.77-2.854.30.35330640.8970.1890.4021.53899.1
2.85-2.934.20.28830210.9210.1560.3291.57999.1
2.93-3.024.20.2330530.9540.1230.2621.54599.1
3.02-3.134.20.18930580.9640.1010.2151.60198.8
3.13-3.264.20.15330620.9770.0830.1751.62198.6
3.26-3.414.20.11730430.9850.0630.1341.6998.4
3.41-3.584.20.09330470.990.050.1071.84697.7
3.58-3.814.30.08130440.9920.0440.0932.00697.3
3.81-4.14.20.07630380.9910.0410.0872.38696.3
4.1-4.524.20.06930000.9920.0380.082.94194.8
4.52-5.174.10.06529870.9930.0360.0753.03293.5
5.17-6.514.20.06629960.9930.0350.0752.34892.3
6.51-504.30.04130400.9970.0220.0471.98686.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.412
Highest resolutionLowest resolution
Rotation41.6 Å2.65 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: 2.399→41.593 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 3125 5.03 %random selection
Rwork0.1683 ---
obs0.1699 62119 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.05 Å2 / Biso mean: 45.4487 Å2 / Biso min: 18.62 Å2
Refinement stepCycle: final / Resolution: 2.399→41.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 108 361 6208
Biso mean--46.39 48.6 -
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076039
X-RAY DIFFRACTIONf_angle_d0.9178176
X-RAY DIFFRACTIONf_chiral_restr0.051858
X-RAY DIFFRACTIONf_plane_restr0.0051042
X-RAY DIFFRACTIONf_dihedral_angle_d17.8173550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3986-2.43610.29231320.25682612274499
2.4361-2.4760.29531300.248826672797100
2.476-2.51870.25081280.235626212749100
2.5187-2.56450.27191180.235126832801100
2.5645-2.61380.26271530.22832599275299
2.6138-2.66720.25821660.21772613277999
2.6672-2.72510.24391450.21462622276799
2.7251-2.78850.24041370.20422629276699
2.7885-2.85820.26761340.20092628276299
2.8582-2.93550.22811510.18962625277699
2.9355-3.02190.22881320.18712634276699
3.0219-3.11940.21951420.18482645278798
3.1194-3.23080.22051460.1832626277299
3.2308-3.36010.22251420.168726982840100
3.3601-3.5130.20511450.149226632808100
3.513-3.69810.17541590.142926842843100
3.6981-3.92960.17451540.132126902844100
3.9296-4.23270.15351340.124327422876100
4.2327-4.65820.15741480.118727432891100
4.6582-5.3310.14551290.12827842913100
5.331-6.7120.18891370.177328192956100
6.712-41.59940.17811630.18582967313099
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)
12.17580.8087-0.17022.4651-0.40131.8053-0.06560.47290.4846-0.13580.07190.1281-0.3394-0.1448-0.05070.33530.07620.03210.33610.10780.4318-63.070952.8875-1.4051
22.31430.5788-0.62930.9615-0.20421.38760.02520.07820.53320.10430.01390.1233-0.28160.0773-0.01070.3946-0.094200.27310.03920.3559-37.663159.4577-2.4294
32.5410.6191-0.93061.1563-0.23211.1637-0.0366-0.00150.1469-0.01010.03360.0188-0.22410.24460.03060.3038-0.084-0.02770.30210.04650.256-35.388851.2074-5.1889
41.27711.3387-0.18282.3848-0.19481.7672-0.02250.04240.10670.00970.06940.21570.1033-0.1186-0.05050.3066-0.03990.04190.25410.06330.2535-45.462923.4118-19.3211
52.155-0.29540.13481.80690.06991.6503-0.21730.0382-0.0786-0.26060.07210.41640.4104-0.67420.12760.4201-0.12680.00570.38610.06160.3659-54.116917.0186-10.6646
60.7090.1079-0.50310.7243-0.05281.9036-0.0924-0.0659-0.07710.03070.0046-0.01270.270.0220.08370.26820.02080.02320.1920.06480.2492-51.49416.21976.4248
72.06580.2452-0.67330.9450.11711.36420.0422-0.02740.07780.0955-0.04950.0946-0.1814-0.06920.01260.29490.03160.04030.21720.02680.2349-55.414731.274711.2441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 128 )A57 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 243 )A129 - 243
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 409 )A244 - 409
4X-RAY DIFFRACTION4chain 'B' and (resid 56 through 131 )B56 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 170 )B132 - 170
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 342 )B171 - 342
7X-RAY DIFFRACTION7chain 'B' and (resid 343 through 409 )B343 - 409

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