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- PDB-4x8q: X-ray crystal structure of AlkD2 from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 4x8q
TitleX-ray crystal structure of AlkD2 from Streptococcus mutans
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / HEAT repeat / ALK motif
Function / homology
Function and homology information


Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #70 / ARM repeat domains / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Phosphomethylpyrimidine kinase / :
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.729 Å
AuthorsMullins, E.A. / Shi, R. / Eichman, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1122098 United States
CitationJournal: Plos One / Year: 2015
Title: A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases.
Authors: Mullins, E.A. / Shi, R. / Kotsch, L.A. / Eichman, B.F.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0405
Polymers24,7941
Non-polymers2464
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.016, 65.091, 87.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 24794.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: Clarke / Gene: ALKD2 / Plasmid: pBG100
Details (production host): Derivative of pET27 encoding a Rhinovirus 3C cleavable hexahistidine tag
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: M2G4T0, UniProt: A0A0M3KL00*PLUS

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 18% (w/v) PEG 3350, 200 mM sodium phosphate, pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.729→50 Å / Num. obs: 31143 / % possible obs: 99.1 % / Redundancy: 8 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.37 / Net I/av σ(I): 42.607 / Net I/σ(I): 11.8 / Num. measured all: 250066
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.73-1.767.40.3834.812960.73884.1
1.76-1.798.20.32715330.705100
1.79-1.838.20.27915710.736100
1.83-1.868.20.24715150.731100
1.86-1.98.20.21815540.771100
1.9-1.958.20.17615540.786100
1.95-28.20.14615390.835100
2-2.058.20.12615610.853100
2.05-2.118.20.10315540.919100
2.11-2.188.20.09115490.966100
2.18-2.268.20.07515561.057100
2.26-2.358.20.07115611.131100
2.35-2.458.20.06315711.214100
2.45-2.588.20.05915671.279100
2.58-2.758.20.05715711.434100
2.75-2.968.10.06315782.15100
2.96-3.267.80.06615843.003100
3.26-3.737.60.0615963.493100
3.73-4.697.80.04716372.73599.9
4.69-507.30.03616961.90298.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: dev_1819)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L9T

3l9t


Resolution: 1.729→40.153 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / Phase error: 16.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1556 5.01 %Random
Rwork0.152 29528 --
obs0.1528 31084 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.62 Å2 / Biso mean: 28.1336 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.729→40.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 13 271 2019
Biso mean--53.29 41.44 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061817
X-RAY DIFFRACTIONf_angle_d0.9742445
X-RAY DIFFRACTIONf_chiral_restr0.042257
X-RAY DIFFRACTIONf_plane_restr0.004309
X-RAY DIFFRACTIONf_dihedral_angle_d12.483716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7293-1.78510.2131380.17382600X-RAY DIFFRACTION99
1.7851-1.84890.1811390.16252656X-RAY DIFFRACTION100
1.8489-1.9230.21121390.16782641X-RAY DIFFRACTION100
1.923-2.01050.18071400.15722654X-RAY DIFFRACTION100
2.0105-2.11650.20531400.15212668X-RAY DIFFRACTION100
2.1165-2.24910.16921410.13942662X-RAY DIFFRACTION100
2.2491-2.42270.1561410.14882687X-RAY DIFFRACTION100
2.4227-2.66640.17561420.16292694X-RAY DIFFRACTION100
2.6664-3.05220.17491420.16462691X-RAY DIFFRACTION100
3.0522-3.84490.15521440.14552732X-RAY DIFFRACTION100
3.8449-40.16360.14791500.14292843X-RAY DIFFRACTION99
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)
13.19520.0071-1.20061.3826-0.30171.8822-0.04190.50040.1049-1.12180.0265-0.1051-0.07010.2013-0.00950.7051-0.04750.12850.32610.02830.22163.739873.29484.8106
27.59431.46013.13974.17752.1956.4419-0.06850.1910.8547-0.82190.0447-0.108-0.92250.20050.0860.47340.0482-0.00640.15210.02510.2423-1.069680.678394.0375
32.53590.25950.00453.62950.41954.5528-0.04460.10360.0311-0.43880.0315-0.0730.0631-0.0261-0.01010.18850.0184-0.01590.0909-0.01310.101-1.159168.121498.0449
43.5316-0.162-2.60144.59450.185.3721-0.0321-0.01210.1761-0.22330.0631-0.0096-0.2589-0.0435-0.05240.11780.0104-0.03780.0993-0.0290.0882-1.291875.4984106.2068
56.9547-0.7256-0.51494.11410.31653.61780.08670.0303-0.32970.2375-0.09290.05850.3653-0.01340.01280.14410.0056-0.0340.107-0.04370.0846-2.078570.4421115.2777
67.26592.055-2.65724.7799-1.50286.72270.0710.07770.38830.1584-0.01280.4151-0.1992-0.6095-0.03230.09340.0184-0.0080.1546-0.04820.153-7.492182.4185117.8822
73.6133-1.481-0.03484.570.56363.22710.1450.053-0.04330.2889-0.0469-0.15910.23660.097-0.04110.1124-0.0048-0.04240.1229-0.02090.08153.616378.1328122.3755
86.3948-2.02534.09592.6335-1.17572.97730.3208-0.920.39650.5589-0.03790.20320.05810.3748-0.11440.2754-0.03450.05810.3528-0.08930.1815-0.787286.0535130.6366
96.5547-2.8991.38922.6235-2.13024.37170.1393-0.2250.2250.2933-0.033-0.460.08390.2041-0.22470.1969-0.0379-0.08450.2293-0.06530.187810.660381.6587129.2548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 14 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 32 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 83 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 101 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 128 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 141 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 173 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 185 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 186 through 206 )A0

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