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- PDB-6aw8: 2.25A resolution domain swapped dimer structure of SAH bound cate... -

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Basic information

Entry
Database: PDB / ID: 6aw8
Title2.25A resolution domain swapped dimer structure of SAH bound catechol O-methyltransferase (COMT) from Nannospalax galili
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Spalax / COMT / S-adenosylmethionine binding
Function / homology
Function and homology information


catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / dopamine metabolic process / methylation / axon / dendrite / magnesium ion binding / plasma membrane
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNannospalax galili (Upper Galilee mountains blind mole rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Deng, Y. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: Crystal structure of the catechol-o-methyl transferase (COMT) enzyme of the subterranean mole rat (Spalax) and the effect of L136M substitution
Authors: Deng, Y. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4269
Polymers77,1523
Non-polymers1,2736
Water2,666148
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,7171
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,7171
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,7171
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.643, 97.531, 104.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase / COMT


Mass: 25717.373 Da / Num. of mol.: 3 / Fragment: M43-P262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nannospalax galili (Upper Galilee mountains blind mole rat)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A452CSQ0*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.1 Å3/Da / Density % sol: 60.38 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.4 % (w/v) PEG 8000, 80 mM sodium cacodylate, 160 mM calcium chloride, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.77 Å / Num. obs: 45368 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.9 / Num. measured all: 292792 / Scaling rejects: 3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.906 / Num. unique obs: 4104 / CC1/2: 0.774 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.96 Å48.77 Å
Translation6.96 Å48.77 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIX(dev_2510: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLB

2zlb


Resolution: 2.25→46.197 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2102 2205 4.87 %
Rwork0.1832 --
obs0.1846 45286 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.97 Å2 / Biso mean: 50.0581 Å2 / Biso min: 27.46 Å2
Refinement stepCycle: final / Resolution: 2.25→46.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4947 0 81 148 5176
Biso mean--44.81 53.02 -
Num. residues----637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035142
X-RAY DIFFRACTIONf_angle_d0.6276998
X-RAY DIFFRACTIONf_chiral_restr0.041803
X-RAY DIFFRACTIONf_plane_restr0.003890
X-RAY DIFFRACTIONf_dihedral_angle_d12.9333104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.29890.30311660.27632584275097
2.2989-2.35240.25581300.241627442874100
2.3524-2.41120.3061400.23727032843100
2.4112-2.47640.23281470.218127102857100
2.4764-2.54930.27041300.205927242854100
2.5493-2.63160.2457930.209427602853100
2.6316-2.72560.26271110.21562286239784
2.7256-2.83470.27011410.192627412882100
2.8347-2.96370.23351640.193627022866100
2.9637-3.11990.21621500.192927432893100
3.1199-3.31540.22151290.182227412870100
3.3154-3.57130.22071200.17612629274994
3.5713-3.93050.18221440.16552490263491
3.9305-4.49880.16241300.143228042934100
4.4988-5.66640.15571370.15728132950100
5.6664-46.20670.22451730.202429073080100

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