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- PDB-7m6b: The Crystal Structure of Mcbe1 -

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Basic information

Entry
Database: PDB / ID: 7m6b
TitleThe Crystal Structure of Mcbe1
ComponentsSite-specific DNA-methyltransferase (adenine-specific)
KeywordsTRANSFERASE / methyl transferase
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation
Similarity search - Function
Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / S-ADENOSYLMETHIONINE / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Proteins / Year: 2021
Title: Target highlights in CASP14: Analysis of models by structure providers.
Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / ...Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / Fidelis, K. / Grinter, R. / Gupta, G.D. / Hartmann, M.D. / Hayes, C.S. / Heidebrecht, T. / Ilari, A. / Joachimiak, A. / Kim, Y. / Linares, R. / Lovering, A.L. / Lunin, V.V. / Lupas, A.N. / Makbul, C. / Michalska, K. / Moult, J. / Mukherjee, P.K. / Nutt, W.S. / Oliver, S.L. / Perrakis, A. / Stols, L. / Tainer, J.A. / Topf, M. / Tsutakawa, S.E. / Valdivia-Delgado, M. / Schwede, T.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Site-specific DNA-methyltransferase (adenine-specific)
A: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9697
Polymers67,6632
Non-polymers1,3055
Water7,080393
1
B: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6143
Polymers33,8321
Non-polymers7832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3544
Polymers33,8321
Non-polymers5233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.446, 73.750, 160.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 266 / Label seq-ID: 1 - 266

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Site-specific DNA-methyltransferase (adenine-specific)


Mass: 33831.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria)
Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_2437 / Production host: Escherichia coli (E. coli)
References: UniProt: B9MNH4, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M Citric acid pH 4.0 and 1.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5419 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 26, 2013 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→43.429 Å / Num. obs: 50187 / % possible obs: 100 % / Redundancy: 6.39 % / Rsym value: 0.0766 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.07 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7031 / Rsym value: 0.5786 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOLREPphasing
PROTEUM PLUSdata scaling
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPM

2dpm


Resolution: 1.9→43.429 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.506 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2436 2498 4.989 %
Rwork0.2057 47568 -
all0.208 --
obs-50066 99.858 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.451 Å20 Å20 Å2
2--1.69 Å2-0 Å2
3----1.239 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 88 393 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173908
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6495637
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5838990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76522.768224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69115703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5951520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
X-RAY DIFFRACTIONr_nbd_refined0.2060.2867
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23729
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1550.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.217
X-RAY DIFFRACTIONr_nbd_other0.2110.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.214
X-RAY DIFFRACTIONr_mcbond_it2.6522.9641938
X-RAY DIFFRACTIONr_mcbond_other2.6522.9641938
X-RAY DIFFRACTIONr_mcangle_it3.9264.4222412
X-RAY DIFFRACTIONr_mcangle_other3.9264.4232413
X-RAY DIFFRACTIONr_scbond_it3.2893.2822234
X-RAY DIFFRACTIONr_scbond_other3.2893.2822234
X-RAY DIFFRACTIONr_scangle_it5.1554.773225
X-RAY DIFFRACTIONr_scangle_other5.1544.7693226
X-RAY DIFFRACTIONr_lrange_it7.38434.6314918
X-RAY DIFFRACTIONr_lrange_other7.30134.2794831
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.057465
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.129780.05007
12AX-RAY DIFFRACTIONLocal ncs0.129780.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3511800.3323463X-RAY DIFFRACTION99.8082
1.949-2.0030.3241790.3113398X-RAY DIFFRACTION99.9721
2.003-2.0610.3311530.2833299X-RAY DIFFRACTION99.9132
2.061-2.1240.3051740.2743170X-RAY DIFFRACTION99.9104
2.124-2.1940.291580.2493122X-RAY DIFFRACTION99.9086
2.194-2.2710.2581750.2293003X-RAY DIFFRACTION99.9685
2.271-2.3560.2731530.232865X-RAY DIFFRACTION99.8346
2.356-2.4520.2731330.2082831X-RAY DIFFRACTION99.798
2.452-2.5610.2671490.2122671X-RAY DIFFRACTION99.8937
2.561-2.6860.2751300.1922576X-RAY DIFFRACTION99.8524
2.686-2.8310.2191350.1862457X-RAY DIFFRACTION99.8075
2.831-3.0030.2341260.1842314X-RAY DIFFRACTION99.9181
3.003-3.210.2391160.1942208X-RAY DIFFRACTION99.914
3.21-3.4670.2411150.1852046X-RAY DIFFRACTION99.5853
3.467-3.7970.214870.1791894X-RAY DIFFRACTION99.7482
3.797-4.2440.18950.1591720X-RAY DIFFRACTION99.9449
4.244-4.8980.207860.151545X-RAY DIFFRACTION99.8775
4.898-5.9930.185740.1751311X-RAY DIFFRACTION100
5.993-8.4520.21500.2051049X-RAY DIFFRACTION100
8.452-43.4290.3300.256626X-RAY DIFFRACTION98.6466

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