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- PDB-3cc8: Crystal structure of a putative methyltransferase (bce_1332) from... -

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Basic information

Entry
Database: PDB / ID: 3cc8
TitleCrystal structure of a putative methyltransferase (bce_1332) from bacillus cereus atcc 10987 at 1.64 A resolution
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / Putative methyltransferase from ndp-n-methyl-l-glucosamine biosynthetic pathway / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyMethyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICKEL (II) ION / Uncharacterized protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative methyltransferase from NDP-N-methyl-L-glucosamine biosynthetic pathway (NP_977653.1) from Bacillus cereus ATCC 10987 at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_label_seq_id / _struct_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6313
Polymers26,5131
Non-polymers1172
Water3,135174
1
A: Putative methyltransferase
hetero molecules

A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2616
Polymers53,0272
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3190 Å2
ΔGint-20.5 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.223, 54.399, 52.751
Angle α, β, γ (deg.)90.000, 109.500, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative methyltransferase /


Mass: 26513.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: NP_977653.1, BCE_1332 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q73BT6
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 40.0% MPD, 5.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97964, 0.97978
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979641
30.979781
ReflectionResolution: 1.64→28.194 Å / Num. obs: 29308 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.775 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.683.90.7920.9815320990.79296.8
1.68-1.733.90.5971.2809720880.59797.1
1.73-1.783.90.4711.6786320280.47197.2
1.78-1.833.90.3712766719790.37197.5
1.83-1.893.90.2782.7746119230.27897.6
1.89-1.963.90.2093.5714018460.20997.8
1.96-2.033.90.1554.7704018180.15598
2.03-2.123.90.1295.5674317450.12998.2
2.12-2.213.90.1136.3636416420.11398.2
2.21-2.323.90.0967.3615815950.09698.5
2.32-2.443.90.0868589715260.08698.6
2.44-2.593.90.088.3552914310.0898.7
2.59-2.773.90.0729.1527113680.07298.8
2.77-2.993.80.06410484112610.06499
2.99-3.283.80.05710.6451611800.05799.2
3.28-3.673.80.05112.3402910580.05199.3
3.67-4.233.80.04513.736239540.04599.4
4.23-5.193.80.04314.329837950.04399.7
5.19-7.333.70.04813.423216290.04899.6
7.33-28.1943.50.05111.911873430.05195.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.64→28.194 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.814 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO NI ATOMS OF THE A SUBUNIT WERE FOUND IN THE ASYMMETRIC UNIT. THE FIRST NI ATOM WAS COORDINATED TO THE SIDE CHAIN OF HIS 188, GLU 192, AND THREE WATERS. THE OTHER NI ATOM WAS DISORDERED AND DUAL CONFORMATION WERE MODELED. DUAL NI ATOMS WERE COORDINATED TO THE SIDE CHAINS OF HIS 104, HIS 158, GLU 103 AND FOUR WATER MOLECULES. ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE NI IONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1491 5.1 %RANDOM
Rwork0.165 ---
obs0.167 29307 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-1.33 Å2
2---0.19 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.64→28.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 2 174 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221804
X-RAY DIFFRACTIONr_bond_other_d0.0010.021195
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9642462
X-RAY DIFFRACTIONr_angle_other_deg0.98132940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04124.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44115312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.299155
X-RAY DIFFRACTIONr_chiral_restr0.1050.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022051
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
X-RAY DIFFRACTIONr_nbd_refined0.2180.2379
X-RAY DIFFRACTIONr_nbd_other0.1870.21268
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2899
X-RAY DIFFRACTIONr_nbtor_other0.0870.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2139
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.221
X-RAY DIFFRACTIONr_mcbond_it2.48131215
X-RAY DIFFRACTIONr_mcbond_other0.5683449
X-RAY DIFFRACTIONr_mcangle_it3.03951812
X-RAY DIFFRACTIONr_scbond_it5.6098768
X-RAY DIFFRACTIONr_scangle_it7.57411650
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 100 -
Rwork0.262 1998 -
all-2098 -
obs--96.55 %
Refinement TLS params.Method: refined / Origin x: 25.5858 Å / Origin y: 33.1978 Å / Origin z: 14.228 Å
111213212223313233
T-0.0643 Å20.0002 Å20.0244 Å2--0.0506 Å2-0.0075 Å2---0.0729 Å2
L1.3315 °2-0.6809 °21.3495 °2-1.3942 °2-0.6337 °2--1.6335 °2
S0.1014 Å °0.0947 Å °-0.0553 Å °-0.0166 Å °-0.0271 Å °0.0896 Å °0.0595 Å °-0.0054 Å °-0.0743 Å °

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