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- PDB-3g2q: Crystal Structure of the Glycopeptide N-methyltransferase MtfA co... -

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Basic information

Entry
Database: PDB / ID: 3g2q
TitleCrystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with sinefungin
ComponentsPCZA361.24
KeywordsTRANSFERASE / SAM-dependent methyltransferase / glycopeptide antibiotics biosynthesis / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


Carboxypeptidase Inhibitor; Chain A - #60 / HSP40/DNAj peptide-binding domain - #20 / : / HSP40/DNAj peptide-binding domain / Carboxypeptidase Inhibitor; Chain A / Methyltransferase domain 25 / Methyltransferase domain / Other non-globular / Vaccinia Virus protein VP39 / Special ...Carboxypeptidase Inhibitor; Chain A - #60 / HSP40/DNAj peptide-binding domain - #20 / : / HSP40/DNAj peptide-binding domain / Carboxypeptidase Inhibitor; Chain A / Methyltransferase domain 25 / Methyltransferase domain / Other non-globular / Vaccinia Virus protein VP39 / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / PCZA361.24
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Chem.Biol. / Year: 2009
Title: Structure and function of the glycopeptide N-methyltransferase MtfA, a tool for the biosynthesis of modified glycopeptide antibiotics.
Authors: Shi, R. / Lamb, S.S. / Zakeri, B. / Proteau, A. / Cui, Q. / Sulea, T. / Matte, A. / Wright, G.D. / Cygler, M.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PCZA361.24
B: PCZA361.24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8184
Polymers65,0552
Non-polymers7632
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-7 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.611, 71.918, 75.062
Angle α, β, γ (deg.)90.000, 103.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PCZA361.24


Mass: 32527.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Gene: mtfA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52805
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 18% PEG-monomethyl ether 5K, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 31659 / % possible obs: 92.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.043 / Χ2: 0.996 / Net I/σ(I): 22.896
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.18-2.262.40.2921891.001164.1
2.26-2.352.80.25126530.921177.6
2.35-2.463.20.23629981.004188.2
2.46-2.583.50.19933250.989197.7
2.58-2.753.80.15734001.006199.6
2.75-2.963.80.10634281199.8
2.96-3.263.80.06234181.004199.8
3.26-3.733.80.0434430.998199.8
3.73-4.73.80.02834371.008199.8
4.7-503.70.02533680.998195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: PDB ENTRY 3G2M

3g2m


Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.254 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.835 / SU B: 9.649 / SU ML: 0.13 / SU R Cruickshank DPI: 0.284 / SU Rfree: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1589 5 %RANDOM
Rwork0.226 ---
obs0.228 31620 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 116.01 Å2 / Biso mean: 50.357 Å2 / Biso min: 22.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å2-0.02 Å2
2--1.74 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 54 124 3799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223754
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9955086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60322.364165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681543
X-RAY DIFFRACTIONr_chiral_restr0.1010.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022840
X-RAY DIFFRACTIONr_nbd_refined0.2150.21528
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22445
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.23
X-RAY DIFFRACTIONr_mcbond_it0.9231.52457
X-RAY DIFFRACTIONr_mcangle_it1.42723799
X-RAY DIFFRACTIONr_scbond_it1.89231451
X-RAY DIFFRACTIONr_scangle_it3.0174.51285
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 72 -
Rwork0.256 1463 -
all-1535 -
obs--61.16 %
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)
13.17030.22250.61271.98750.83371.49730.03840.0560.2974-0.082-0.11330.2124-0.0849-0.07670.0749-0.14280.0045-0.0049-0.0749-0.0165-0.075-22.66116.6505-34.8336
27.8293-3.8139-3.28164.6747-0.6223.1260.3609-0.27261.81180.3915-0.0605-1.0207-0.62220.2912-0.30040.0138-0.1097-0.02260.0725-0.05960.25112.213316.0005-17.8372
31.76180.4719-0.60241.6527-0.81744.6883-0.1216-0.1266-0.0403-0.0119-0.03840.20290.7665-0.88870.16-0.0318-0.20710.06550.1711-0.1018-0.0907-23.0589-5.6282-9.6417
42.465-0.34710.09390.16680.09231.3642-0.0223-0.1067-0.22810.0235-0.00140.07780.14990.11790.0237-0.0780.00440.0263-0.02820.0227-0.14713.2924-7.9097-16.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 175
2X-RAY DIFFRACTION1A235 - 274
3X-RAY DIFFRACTION2B8 - 32
4X-RAY DIFFRACTION2B206 - 234
5X-RAY DIFFRACTION2A176 - 205
6X-RAY DIFFRACTION3A8 - 37
7X-RAY DIFFRACTION3A206 - 234
8X-RAY DIFFRACTION3B176 - 205
9X-RAY DIFFRACTION4B47 - 175
10X-RAY DIFFRACTION4B235 - 273

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