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- PDB-2yj0: X-ray structure of chemically engineered Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 2yj0
TitleX-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin
ComponentsDODECIN
KeywordsFLAVOPROTEIN / FLAVIN BINDING PROTEIN / PROTEIN-ENGINEERING / PUTATIVE STORAGE PROTEIN / DODECIN HYBRID
Function / homology
Function and homology information


nucleotide binding / extracellular region
Similarity search - Function
Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-420 / COENZYME A / FLAVIN MONONUCLEOTIDE / Dodecin family protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVinzenz, X. / Grosse, W. / Linne, U. / Meissner, B. / Essen, L.-O.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids.
Authors: Vinzenz, X. / Grosse, W. / Linne, U. / Meissner, B. / Essen, L.-O.
History
DepositionMay 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_sheet / 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 / _struct_conn.pdbx_leaving_atom_flag / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DODECIN
B: DODECIN
C: DODECIN
D: DODECIN
E: DODECIN
F: DODECIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,46029
Polymers45,0516
Non-polymers10,41023
Water2,936163
1
A: DODECIN
B: DODECIN
C: DODECIN
D: DODECIN
E: DODECIN
F: DODECIN
hetero molecules

A: DODECIN
B: DODECIN
C: DODECIN
D: DODECIN
E: DODECIN
F: DODECIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,92158
Polymers90,10212
Non-polymers20,81946
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area44540 Å2
ΔGint-181 kcal/mol
Surface area36430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 103.800, 82.500
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
51E
61F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISVALVAL1AA3 - 493 - 49
21HISHISVALVAL1BB3 - 493 - 49
31HISHISVALVAL1CC3 - 493 - 49
41HISHISVALVAL1DD3 - 493 - 49
51HISHISVALVAL1EE3 - 493 - 49
61HISHISVALVAL1FF3 - 493 - 49
12GLYGLYPHEPHE1AA51 - 6451 - 64
22GLYGLYPHEPHE1BB51 - 6451 - 64
32GLYGLYPHEPHE1CC51 - 6451 - 64
42GLYGLYPHEPHE1DD51 - 6451 - 64
52GLYGLYPHEPHE1EE51 - 6451 - 64
62GLYGLYPHEPHE1FF51 - 6451 - 64
13LEULEUASPASP4AA66 - 6866 - 68
23LEULEUASPASP4BB66 - 6866 - 68
33LEULEUASPASP4CC66 - 6866 - 68
43LEULEUASPASP4DD66 - 6866 - 68
53LEULEUASPASP4EE66 - 6866 - 68
63LEULEUASPASP4FF66 - 6866 - 68

NCS oper:
IDCodeMatrixVector
1given(-0.4886, 0.6821, 0.544), (-0.7423, 0.002728, -0.6701), (-0.4586, -0.7312, 0.505)-76.46, 25.79, 21.51
2given(-0.4886, 0.6821, 0.544), (-0.7423, 0.002728, -0.6701), (-0.4586, -0.7312, 0.505)-76.46, 25.79, 21.51
3given(-0.4886, 0.6821, 0.544), (-0.7423, 0.002728, -0.6701), (-0.4586, -0.7312, 0.505)-76.46, 25.79, 21.51
4given(-0.07673, 0.003593, -0.997), (0.005105, -1, -0.003997), (-0.997, -0.005397, 0.07671)-29.83, -42.78, -27.85
5given(-0.07673, 0.003593, -0.997), (0.005105, -1, -0.003997), (-0.997, -0.005397, 0.07671)-29.83, -42.78, -27.85
6given(-0.07673, 0.003593, -0.997), (0.005105, -1, -0.003997), (-0.997, -0.005397, 0.07671)-29.83, -42.78, -27.85
7given(-0.4929, -0.7372, -0.4622), (0.6835, 0.000689, -0.73), (0.5385, -0.6757, 0.5035)-66.54, -42.21, -27.19
8given(-0.4929, -0.7372, -0.4622), (0.6835, 0.000689, -0.73), (0.5385, -0.6757, 0.5035)-66.54, -42.21, -27.19
9given(-0.4929, -0.7372, -0.4622), (0.6835, 0.000689, -0.73), (0.5385, -0.6757, 0.5035)-66.54, -42.21, -27.19
10given(0.507, -0.7258, 0.465), (-0.6789, -0.003943, 0.7342), (-0.531, -0.6879, -0.4947)-26.69, -41.51, 68.6
11given(0.507, -0.7258, 0.465), (-0.6789, -0.003943, 0.7342), (-0.531, -0.6879, -0.4947)-26.69, -41.51, 68.6
12given(0.507, -0.7258, 0.465), (-0.6789, -0.003943, 0.7342), (-0.531, -0.6879, -0.4947)-26.69, -41.51, 68.6
13given(-0.4922, -0.6801, 0.5434), (0.7385, 0.004321, 0.6743), (-0.4609, 0.7331, 0.5001)-44.67, -68.48, 50.49
14given(-0.4922, -0.6801, 0.5434), (0.7385, 0.004321, 0.6743), (-0.4609, 0.7331, 0.5001)-44.67, -68.48, 50.49
15given(-0.4922, -0.6801, 0.5434), (0.7385, 0.004321, 0.6743), (-0.4609, 0.7331, 0.5001)-44.67, -68.48, 50.49

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DODECIN


Mass: 7508.471 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-70 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CYS 59 COVALENTLY MODIFIED WITH N-(2-ETHYL-IODO-ACETAMIDE)-DANSYL
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q8VK10

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Non-polymers , 6 types, 186 molecules

#2: Chemical
ChemComp-420 / N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE


Mass: 461.318 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H20IN3O3S
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN B, THR 60 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN B, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN C, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN D, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN E, THR 60 TO CYS ENGINEERED RESIDUE IN CHAIN F, THR 60 TO CYS
Nonpolymer detailsCOENZYME A (COA): NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE (FMN): NON-COVALENTLY BOUND N-[2-({[5- ...COENZYME A (COA): NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE (FMN): NON-COVALENTLY BOUND N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IOD
Sequence detailsENGINEERED T59C MUTATION, SER 1 IN CHAIN B IS NOT DEFINED IN ELECTRON DENSITY.

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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: 43.1 %
Crystal growDetails: 2M NACL, 2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→47.08 Å / Num. obs: 16225 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIZ NULL

2yiz


Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 20.231 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. COVALENTLY BOUND TO C59 N-(2-ETHYL-IODO-ACETAMIDE)-DANSYL OCCUPIED PARTLY THE FMN BINDING POCKET. IT WAS REFINED IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. COVALENTLY BOUND TO C59 N-(2-ETHYL-IODO-ACETAMIDE)-DANSYL OCCUPIED PARTLY THE FMN BINDING POCKET. IT WAS REFINED IN TWO CONFORMATIONS OF WHICH CONFORMATION A LIES WITHIN THE FMN BINDING POCKET REPLACING THE ORIGINAL COFACTOR. CONFORMATION B, DIRECTING INTO THE SPHERE, SHOWED NO DEFINED DENSITY FOR THE AROMATIC DANSYL MOIETY. THIS PART WAS REFINED WITH ZERO OCCUPANCY ATOMS PRESENT, BEING REMOVED PRIOR TO DEPOSITION OWING TO TECHNICAL REASONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27493 974 6 %RANDOM
Rwork0.21692 ---
obs0.22038 15215 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.829 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---1.29 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 625 163 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213938
X-RAY DIFFRACTIONr_bond_other_d0.0030.022414
X-RAY DIFFRACTIONr_angle_refined_deg1.1562.1235393
X-RAY DIFFRACTIONr_angle_other_deg0.7535705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00223.208159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97515516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5421530
X-RAY DIFFRACTIONr_chiral_restr0.0640.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it0.0841.52031
X-RAY DIFFRACTIONr_mcbond_other0.0271.5854
X-RAY DIFFRACTIONr_mcangle_it0.19423246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.54631907
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9874.52138
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A762tight positional0.170.05
2B762tight positional0.20.05
3C762tight positional0.150.05
4D762tight positional0.240.05
5E762tight positional0.170.05
6F762tight positional0.20.05
1A41medium positional0.220.5
2B41medium positional0.140.5
3C41medium positional0.170.5
4D41medium positional0.150.5
5E41medium positional0.240.5
6F41medium positional0.140.5
1A762tight thermal0.110.5
2B762tight thermal0.090.5
3C762tight thermal0.090.5
4D762tight thermal0.10.5
5E762tight thermal0.090.5
6F762tight thermal0.070.5
1A41medium thermal0.112
2B41medium thermal0.112
3C41medium thermal0.072
4D41medium thermal0.112
5E41medium thermal0.082
6F41medium thermal0.072
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 65 -
Rwork0.281 1101 -
obs--99.91 %
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)
17.1741-2.48060.56753.2177-0.90642.06750.1599-0.0257-0.0831-0.117-0.0681-0.0888-0.07260.1498-0.09180.1376-0.06780.01590.0676-0.01050.0155-35.0583-6.8379.6485
25.1884.0019-0.0057.55210.10861.87030.01030.1328-0.0701-0.02220.0089-0.06690.0043-0.0817-0.01920.11130.0577-0.00710.0785-0.02070.0082-48.8312-22.7249-1.0927
31.9763-0.58920.61522.1283-2.29648.0484-0.08790.1383-0.0688-0.0188-0.0974-0.17750.09210.03440.18540.0743-0.00440.05010.0655-0.07910.1719-36.7932-36.1498.0844
42.0729-0.981-1.39033.23182.90466.60930.05060.10020.0191-0.0248-0.09170.0564-0.2908-0.08640.04110.05340.0263-0.01460.08890.04970.0918-58.6226-5.304311.6895
57.3323-2.9774-1.53924.96410.79662.8139-0.0063-0.159-0.2813-0.0782-0.0206-0.02170.142-0.13850.02690.1615-0.0520.01680.051-0.02690.0698-56.8202-37.65849.9245
62.7123-0.27320.42076.261-3.16214.3621-0.0910.1229-0.0965-0.02080.07140.1628-0.0547-0.28870.01960.00660.00560.01190.1708-0.06280.1123-68.8838-20.204520.295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 69
2X-RAY DIFFRACTION2B1 - 69
3X-RAY DIFFRACTION3C1 - 69
4X-RAY DIFFRACTION4D1 - 69
5X-RAY DIFFRACTION5E1 - 69
6X-RAY DIFFRACTION6F1 - 69

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