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- PDB-4ac8: R2-like ligand binding Mn-Fe oxidase from M. tuberculosis with an... -

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Basic information

Entry
Database: PDB / ID: 4ac8
TitleR2-like ligand binding Mn-Fe oxidase from M. tuberculosis with an organized C-terminal helix
ComponentsR2-LIKE LIGAND BINDING OXIDASE
KeywordsOXIDOREDUCTASE / DIMETAL COFACTOR / MONOOXYGENASE / METALLOPROTEIN
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / Oxidoreductases / manganese ion binding / oxidoreductase activity / iron ion binding / identical protein binding / cytosol
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / MYRISTIC ACID / R2-like ligand binding oxidase / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAndersson, C.S. / Berthold, C.L. / Hogbom, M.
CitationJournal: Chem.Biodivers. / Year: 2012
Title: A Dynamic C-Terminal Segment in the Mycobacterium Tuberculosis Mn/Fe R2Lox Protein Can Adopt a Helical Structure with Possible Functional Consequences.
Authors: Andersson, C.S. / Berthold, C.L. / Hogbom, M.
History
DepositionDec 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Nov 20, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 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 / struct_ncs_dom_lim / 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_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.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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 / _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: R2-LIKE LIGAND BINDING OXIDASE
B: R2-LIKE LIGAND BINDING OXIDASE
C: R2-LIKE LIGAND BINDING OXIDASE
D: R2-LIKE LIGAND BINDING OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,67019
Polymers147,1414
Non-polymers1,52915
Water1,58588
1
C: R2-LIKE LIGAND BINDING OXIDASE
D: R2-LIKE LIGAND BINDING OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2498
Polymers73,5702
Non-polymers6786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-53.2 kcal/mol
Surface area21820 Å2
MethodPISA
2
A: R2-LIKE LIGAND BINDING OXIDASE
B: R2-LIKE LIGAND BINDING OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,42111
Polymers73,5702
Non-polymers8519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-50.2 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.990, 210.850, 139.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 310 / Label seq-ID: 11 - 319

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(-1, 0.002), (-1, -0.016), (0.002, -0.016, 1)8.38358, 105.41907, 0.79889
2given(-0.576, -0.817, 0.022), (-0.816, 0.577, 0.04), (-0.045, 0.005, -0.999)22.03534, 77.798, 40.16528
3given(0.577, 0.817, 0.006), (0.816, -0.577, 0.032), (0.029, -0.014, -0.999)-14.13584, 26.17659, 37.80369

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
R2-LIKE LIGAND BINDING OXIDASE / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT HOMOLOG / RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT HOMOLOG


Mass: 36785.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN V71 (CB) AND Y162 (OH) / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96416, UniProt: P9WH69*PLUS, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 103 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.127
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.75→36.72 Å / Num. obs: 39247 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 49.379 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.75
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.83 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EE4

3ee4


Resolution: 2.75→36.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.585 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF RESIDUE V71 AND Y162 ARE COVALENTLY CROSSLINKED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1963 5 %RANDOM
Rwork0.22 ---
obs0.222 37284 92.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---1.2 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.75→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9939 0 80 88 10107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.94813870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.41951235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77623.015544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.546151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.64215108
X-RAY DIFFRACTIONr_chiral_restr0.080.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2481 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.280.5
2Bmedium positional0.290.5
3Cmedium positional0.280.5
4Dmedium positional0.310.5
1Amedium thermal5.862
2Bmedium thermal6.212
3Cmedium thermal6.882
4Dmedium thermal5.522
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 139 -
Rwork0.266 2659 -
obs--94.18 %

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