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- PDB-2ux9: Crystal structure of the T. thermophilus dodecin R65A mutant -

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Basic information

Entry
Database: PDB / ID: 2ux9
TitleCrystal structure of the T. thermophilus dodecin R65A mutant
ComponentsDODECIN
KeywordsFLAVOPROTEIN
Function / homology
Function and homology information


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 / PHOSPHATE ION / Dodecin
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMeissner, B. / Essen, L.-O.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Dodecin from Thermus Thermophilus, a Bifunctional Cofactor Storage Protein.
Authors: Meissner, B. / Schleicher, E. / Weber, S. / Essen, L.-O.
History
DepositionMar 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Other
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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_symmetry / _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_symmetry / _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_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)53,76325
Polymers46,0436
Non-polymers7,72019
Water9,170509
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)107,52650
Polymers92,08612
Non-polymers15,44038
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area40330 Å2
ΔGint-148.6 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.585, 67.585, 169.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.17815, -0.6781, -0.71305), (-0.67889, -0.60925, 0.40978), (-0.7123, 0.41109, -0.56889)26.17493, 45.60958, -0.08363
2given(0.89002, 0.37465, 0.25981), (-0.05097, -0.48453, 0.87329), (0.45306, -0.79049, -0.41215)-7.19316, 34.67849, 11.91695
3given(-0.28991, -0.71894, -0.63173), (-0.30789, 0.69505, -0.6497), (0.90618, 0.00615, -0.42285)33.1838, 11.29104, -12.28365
4given(-0.12376, -0.37867, -0.91722), (0.95975, -0.28052, -0.01369), (-0.25211, -0.882, 0.39814)23.35889, 16.59588, 23.07646
5given(0.88998, -0.05577, 0.45258), (0.37218, -0.48461, -0.7916), (0.26347, 0.87295, -0.41054)2.77646, 28.87946, -23.57622

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DODECIN


Mass: 7673.815 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q5SIE3

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Non-polymers , 5 types, 528 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 65 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN C, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN E, ARG 65 TO ALA ENGINEERED RESIDUE IN CHAIN F, ARG 65 TO ALA
Nonpolymer detailsCOENZYME A (COA): BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE (FMN): ...COENZYME A (COA): BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE (FMN): BOUND AS DIMERS ALONG THE TWOFOLD SYMMETRY AXES

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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: 1.88 Å3/Da / Density % sol: 34.08 % / Description: NONE
Crystal growDetails: 0.4 M AMMONIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9774
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.4→14.88 Å / Num. obs: 87239 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOG

1mog


Resolution: 1.4→14.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.603 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO NONCRYSTALLOGRAPHIC SYMMETRY RESTRAINTS USED DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1575 1.8 %RANDOM
Rwork0.17 ---
obs0.17 85624 98 %-
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: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 493 509 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223788
X-RAY DIFFRACTIONr_bond_other_d0.0020.022462
X-RAY DIFFRACTIONr_angle_refined_deg1.4272.1275184
X-RAY DIFFRACTIONr_angle_other_deg0.87636031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.58924.342152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1115634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1871525
X-RAY DIFFRACTIONr_chiral_restr0.0750.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_nbd_refined0.1980.2575
X-RAY DIFFRACTIONr_nbd_other0.2010.22785
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21736
X-RAY DIFFRACTIONr_nbtor_other0.0830.21977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2408
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.243
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.297
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6541.52011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22423203
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7532010
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8424.51971
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: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 126
Rwork0.214 6090
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)
10.8628-0.63550.10010.9605-0.16740.18330.02610.08170.065-0.0015-0.0447-0.0515-0.00470.07510.0186-0.0397-0.00520.00310.00640.006-0.007832.656429.9959-7.4769
20.64970.2316-0.45920.5557-0.3841.16860.02430.0105-0.0783-0.052800.01130.12940.0828-0.0243-0.0180.0207-0.0176-0.0249-0.0073-0.007117.01532.0909-6.8191
30.55630.2652-0.51980.3582-0.41331.38940.0045-0.03040.10120.04580.0377-0.0233-0.04580.0453-0.0422-0.01490.016-0.0059-0.0239-0.0232-0.00826.542532.44214.8392
40.7102-0.49650.20710.8603-0.33780.31960.01960.0611-0.07530.0053-0.00720.05350.0321-0.0308-0.0125-0.02810.0035-0.0126-0.0061-0.0063-0.0102-1.73613.9504-13.9386
52.12390.2880.58640.31170.12810.5405-0.05620.16580.0382-0.06770.0429-0.00460.00210.05190.0133-0.0290.00500.01190.0036-0.030519.33119.6256-20.8801
60.46-0.0730.210.87340.51970.84050.0091-0.0113-0.0140.05380.0185-0.04240.04110.0352-0.0276-0.01980.0162-0.0015-0.0193-0.0064-0.013931.226211.27885.6207
70.0634-0.1033-0.69611.2983-0.531110.10280.0302-0.04840.26990.024-0.197-0.2817-0.31550.12930.1668-0.01660.01080-0.0350.01270.051925.263643.0419-3.1836
81.5649-3.08440.66929.43765.616614.6098-0.1322-0.227-0.09590.4060.13020.1717-0.02860.18330.0020.01160.01620.0143-0.01570.0005-0.023621.564920.001621.9283
919.3875-4.3196-2.35347.1893.46971.67890.35470.39530.4918-0.3844-0.04610.0329-0.15020.2197-0.3086-0.01150.00960.0057-0.00190.0462-0.02260.815727.8421-19.5711
104.08391.9756-4.46054.3405-3.045.1017-0.05770.0876-0.1144-0.0085-0.0342-0.1510.11950.23720.0919-0.04930.0142-0.00970.0348-0.0134-0.013931.704915.1409-12.5412
111.5237-0.3952-0.78199.045-0.08272.13980.02160.06080.0201-0.09220.0186-0.21350.24220.0924-0.0403-0.01220.0149-0.00580.0003-0.0177-0.029130.49979.6583-9.4172
123.4157-2.03622.44396.3882-3.11765.3299-0.0174-0.0794-0.3046-0.06790.08740.38280.1618-0.2613-0.07-0.0298-0.01220.0136-0.02440.01620.00253.78430.92111.4797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 67
2X-RAY DIFFRACTION2B2 - 67
3X-RAY DIFFRACTION3C2 - 69
4X-RAY DIFFRACTION4D2 - 69
5X-RAY DIFFRACTION5E2 - 67
6X-RAY DIFFRACTION6F2 - 69
7X-RAY DIFFRACTION7A1069
8X-RAY DIFFRACTION8C1073
9X-RAY DIFFRACTION9D1070
10X-RAY DIFFRACTION10E1069
11X-RAY DIFFRACTION11E1070
12X-RAY DIFFRACTION12B1070

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