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- PDB-2yiz: X-ray structure of Mycobacterium tuberculosis Dodecin -

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Basic information

Entry
Database: PDB / ID: 2yiz
TitleX-ray structure of Mycobacterium tuberculosis Dodecin
ComponentsDODECIN
KeywordsFLAVOPROTEIN / FLAVIN BINDING PROTEIN / PROTEIN-ENGINEERING / PUTATIVE STORAGE PROTEIN
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
COENZYME A / FLAVIN MONONUCLEOTIDE / Dodecin family protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 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_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_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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,57520
Polymers30,0264
Non-polymers5,54916
Water4,702261
1
A: DODECIN
B: DODECIN
C: DODECIN
D: DODECIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)106,72460
Polymers90,07712
Non-polymers16,64748
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area47940 Å2
ΔGint-182.4 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.302, 94.302, 230.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-1072-

GOL

21C-1071-

TRS

31C-1071-

TRS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISARGARGAA3 - 283 - 28
21HISHISARGARGBB3 - 283 - 28
31HISHISARGARGCC3 - 283 - 28
41HISHISARGARGDD3 - 283 - 28
12LEULEUHISHISAA36 - 5536 - 55
22LEULEUHISHISBB36 - 5536 - 55
32LEULEUHISHISCC36 - 5536 - 55
42LEULEUHISHISDD36 - 5536 - 55
13GLNGLNARGARGAA57 - 6557 - 65
23GLNGLNARGARGBB57 - 6557 - 65
33GLNGLNARGARGCC57 - 6557 - 65
43GLNGLNARGARGDD57 - 6557 - 65

NCS oper:
IDCodeMatrixVector
1given(0.4998, 0.8662, -0.000125), (0.2889, -0.1666, 0.9428), (0.8166, -0.4712, -0.3335)-47.14, 27.19, 76.98
2given(0.4998, 0.8662, -0.000125), (0.2889, -0.1666, 0.9428), (0.8166, -0.4712, -0.3335)-47.14, 27.19, 76.98
3given(0.4998, 0.8662, -0.000125), (0.2889, -0.1666, 0.9428), (0.8166, -0.4712, -0.3335)-47.14, 27.19, 76.98
4given(0.5005, -0.8658, -9.2E-5), (-0.2886, -0.1669, 0.9428), (-0.8162, -0.4718, -0.3334)47.12, 27.23, 76.97
5given(0.5005, -0.8658, -9.2E-5), (-0.2886, -0.1669, 0.9428), (-0.8162, -0.4718, -0.3334)47.12, 27.23, 76.97
6given(0.5005, -0.8658, -9.2E-5), (-0.2886, -0.1669, 0.9428), (-0.8162, -0.4718, -0.3334)47.12, 27.23, 76.97
7given(0.4999, 0.2886, 0.8166), (0.8661, -0.1666, -0.4714), (3.9E-5, 0.9428, -0.3333)-0.00239, -54.43, 76.97
8given(0.4999, 0.2886, 0.8166), (0.8661, -0.1666, -0.4714), (3.9E-5, 0.9428, -0.3333)-0.00239, -54.43, 76.97
9given(0.4999, 0.2886, 0.8166), (0.8661, -0.1666, -0.4714), (3.9E-5, 0.9428, -0.3333)-0.00239, -54.43, 76.97

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DODECIN


Mass: 7506.432 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q8VK10

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Non-polymers , 6 types, 277 molecules

#2: Chemical
ChemComp-COA / COENZYME A


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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCOENZYME A (COA): NON-COVALENTLY BOUND, NOT COMPLETELY DEFINED IN DENSITY AND THEREFORE ONLY PARTLY ...COENZYME A (COA): NON-COVALENTLY BOUND, NOT COMPLETELY DEFINED IN DENSITY AND THEREFORE ONLY PARTLY REFINED FLAVIN MONONUCLEOTIDE (FMN): NON-COVALENTLY BOUND GLYCEROL (GOL): IN CASE OF F1, F4, F5 ELECTRON DENSITY ALONG 3-FOLD AXIS WAS INTERPRETED AS GLYCEROL 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS): ELECTRON DENSITY ALONG 3-FOLD AXIS WAS INTERPRETED AS TRIS

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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: 3.18 Å3/Da / Density % sol: 61.37 % / Description: NONE
Crystal growpH: 5
Details: 10 MM CO CL2, 100 MM NAOAC PH 5.0, 200 MM HEXANEDIOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9184
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Feb 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→14.91 Å / Num. obs: 43832 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V21

2v21


Resolution: 1.7→14.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.046 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA ALONG THREEFOLD AXIS WAS ONLY PARTLY DEFINED IN ELECTRON DENSITY AND THEREFORE ONLY PARTLY REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19743 1084 2.5 %RANDOM
Rwork0.17198 ---
obs0.17261 42659 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 204 261 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212458
X-RAY DIFFRACTIONr_bond_other_d0.0020.021585
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.0233344
X-RAY DIFFRACTIONr_angle_other_deg0.78833842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77723.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05915370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8671520
X-RAY DIFFRACTIONr_chiral_restr0.070.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
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_it0.8311.51403
X-RAY DIFFRACTIONr_mcbond_other0.2091.5593
X-RAY DIFFRACTIONr_mcangle_it1.50422248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13431055
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6424.51087
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: 728 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.010.05
2Btight positional0.010.05
3Ctight positional0.010.05
4Dtight positional0.010.05
1Atight thermal0.060.5
2Btight thermal0.050.5
3Ctight thermal0.070.5
4Dtight thermal0.060.5
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 73 -
Rwork0.196 3104 -
obs--98.79 %
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)
10.84590.01680.48581.11560.17943.1124-0.0650.0643-0.0424-0.0710.0053-0.26690.05920.4230.05970.05260.00050.01890.13370.0040.073421.450.04955.985
21.02880.3309-0.22613.5988-0.55260.98980.0024-0.28030.00250.41240.0072-0.1597-0.10440.0873-0.00960.1105-0.0032-0.03740.1241-0.00290.023710.74.67275.896
31.06570.15580.0133.2614-1.38971.5701-0.00840.2044-0.1167-0.2897-0.0043-0.3130.21270.17230.01270.1150.02180.03070.1037-0.03020.056210.822-7.97840.741
43.1397-0.9403-0.70891.14490.20641.31090.0599-0.01660.3977-0.0866-0.0297-0.1366-0.30920.0788-0.03010.1172-0.02150.0010.0533-0.0090.0889.20419.63658.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B1 - 101
3X-RAY DIFFRACTION3C1 - 101
4X-RAY DIFFRACTION4D1 - 101

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