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- PDB-2vli: Structure of Deinococcus radiodurans tunicamycin resistance protein -

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Basic information

Entry
Database: PDB / ID: 2vli
TitleStructure of Deinococcus radiodurans tunicamycin resistance protein
ComponentsANTIBIOTIC RESISTANCE PROTEIN
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE
Function / homologyAAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / : / Antibiotic resistance protein
Function and homology information
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMacedo, S. / Kapp, U. / Leiros, I. / Hall, D.R. / Mitchell, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Deinococcus Radiodurans Tunicamycin-Resistance Protein (Tmrd), a Phosphotransferase.
Authors: Kapp, U. / Macedo, S. / Hall, D.R. / Leiros, I. / Mcsweeney, S.M. / Mitchell, E.
History
DepositionJan 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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 / _struct_conn.ptnr2_label_seq_id / _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: ANTIBIOTIC RESISTANCE PROTEIN
B: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9894
Polymers40,8412
Non-polymers1482
Water4,071226
1
A: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules

A: ANTIBIOTIC RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1376
Polymers40,8412
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area20430 Å2
MethodPQS
2
B: ANTIBIOTIC RESISTANCE PROTEIN

B: ANTIBIOTIC RESISTANCE PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,8412
Polymers40,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area920 Å2
ΔGint0.6 kcal/mol
Surface area21150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.360, 118.160, 81.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2052-

HOH

21B-2125-

HOH

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Components

#1: Protein ANTIBIOTIC RESISTANCE PROTEIN / TUNICAMYCIN RESISTANCE PROTEIN


Mass: 20420.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUG7
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCADMIUM ION (CD): FROM CRYSTALLISATION CONDITIONS CHLORIDE ION (CL): FROM CRYSTALLISATION CONDITIONS
Sequence detailsPROTEIN WAS EXPRESSED USING A CONSTRUCT GIVING A PRODUCT WITH A C-TERMINAL TRUNCATION FROM RESIDUE ...PROTEIN WAS EXPRESSED USING A CONSTRUCT GIVING A PRODUCT WITH A C-TERMINAL TRUNCATION FROM RESIDUE 184 FORWARDS.

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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: 2.16 Å3/Da / Density % sol: 48.4 %
Description: PHASING DATA WERE COLLECTED FROM A SECOND CRYSTAL. THE INITIAL MODEL WAS THEN TRANSFERRED TO HIGHER RESOLUTION DATA SET FROM ANOTHER CRYSTAL FOR REFINEMENT.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 DEGREESC AFTER 3-6 DAYS USING HANGING DROPS CONTAINING 2 MICROL OF THE PROTEIN, 0.4-0.8 MICROL 0.1 M CDCL2 AND 1.6-1.2 MICROL OF A RESERVOIR SOLUTION CONTAINING 11-13% PEG 4000, 0.8 M ...Details: 20 DEGREESC AFTER 3-6 DAYS USING HANGING DROPS CONTAINING 2 MICROL OF THE PROTEIN, 0.4-0.8 MICROL 0.1 M CDCL2 AND 1.6-1.2 MICROL OF A RESERVOIR SOLUTION CONTAINING 11-13% PEG 4000, 0.8 M SODIUM FORMATE AND 0.1 M SODIUM ACETATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9144, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2006 / Details: RH COATED TOROIDAL MIRROR
RadiationMonochromator: SI DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91441
20.97921
ReflectionResolution: 1.95→22.93 Å / Num. obs: 28689 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 4.94 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.54
Reflection shellResolution: 1.95→1.97 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→22.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.354 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL HIS-TAGS AND RESIDUES TO A4 AND B3 AND FROM A176 AND B176 WERE NOT VISIBLE IN THE DENSITY MAPS. RESIDUES A15-18 AND A126-129 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL HIS-TAGS AND RESIDUES TO A4 AND B3 AND FROM A176 AND B176 WERE NOT VISIBLE IN THE DENSITY MAPS. RESIDUES A15-18 AND A126-129 WERE ALSO NOT VISIBLE. ALL THESE RESIDUES WERE THEREFORE NOT INCLUDED IN THE STRUCTURE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1486 5.2 %RANDOM
Rwork0.174 ---
obs0.176 27186 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---2.53 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 226 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212699
X-RAY DIFFRACTIONr_bond_other_d0.0060.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9643672
X-RAY DIFFRACTIONr_angle_other_deg0.98434524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3195337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16222.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811527
X-RAY DIFFRACTIONr_chiral_restr0.10.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
X-RAY DIFFRACTIONr_nbd_refined0.2160.2554
X-RAY DIFFRACTIONr_nbd_other0.2070.21930
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21299
X-RAY DIFFRACTIONr_nbtor_other0.0880.21353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9591.52020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93322727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.20631088
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8214.5943
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 102
Rwork0.2 1987

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