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- PDB-6mfm: Structure of thiamine-monophosphate kinase from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 6mfm
TitleStructure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP), orthorhombic crystal form
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Thiamine-monophosphate kinase / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.
Authors: Sullivan, A.H. / Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E. / Abendroth, J.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionSep 26, 2018ID: 5D9U
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_conn_angle / struct_conn
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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine-monophosphate kinase
B: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,71118
Polymers68,7202
Non-polymers1,99116
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-209 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.150, 93.920, 73.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiamine-monophosphate kinase / Thiamine-phosphate kinase


Mass: 34359.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: thiL, ABUW_0092, CBI29_03781 / Plasmid: AcbaC.17905.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5YC82, thiamine-phosphate kinase

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Non-polymers , 5 types, 468 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1 scrren, B1: 20% PEG 4000, 600mM NaCl, 100mM MES/NaOH: AnphA.17905.a.B1.PW37686 at 30mg/ml, 5mM each MgCl2, ADO and TPP: cryo: 20% EG, 5mM MgCl2/ADP/TPP: tray 264489b1, puck ute6-14

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→41.34 Å / Num. obs: 48167 / % possible obs: 99.6 % / Redundancy: 5.284 % / Biso Wilson estimate: 29.655 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.053 / Χ2: 0.935 / Net I/σ(I): 25.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.2150.5242.6634210.7840.62697.5
1.95-23.3140.4583.0133790.850.54498.3
2-2.063.3980.3514.0933290.8960.41699.5
2.06-2.123.6230.2585.7132450.9420.30399.9
2.12-2.194.3280.2217.7131690.960.253100
2.19-2.274.6770.17110.2830430.9770.193100
2.27-2.364.850.15411.529590.9830.17399.9
2.36-2.455.0680.12713.7128350.9890.14299.9
2.45-2.565.3250.10916.1827400.9910.12199.9
2.56-2.695.7370.08919.7226140.9950.099100
2.69-2.836.4250.07723.6125070.9970.083100
2.83-37.280.0630.5623770.9980.065100
3-3.217.2940.04439.0922230.9990.047100
3.21-3.477.2880.03251.26207510.034100
3.47-3.87.260.02566.8193810.027100
3.8-4.257.2380.02274.45174610.024100
4.25-4.917.1520.01885.47156310.01999.9
4.91-6.017.080.02172.92132610.023100
6.01-8.56.8550.0271.37106510.02299.9
8.5-41.345.9760.01597.3461310.01798.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14rc1_3161)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5cc8

5cc8


Resolution: 1.9→41.34 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.84
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2050 4.26 %0
Rwork0.1641 ---
obs0.1662 48155 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.67 Å2 / Biso mean: 28.4197 Å2 / Biso min: 9.11 Å2
Refinement stepCycle: final / Resolution: 1.9→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4573 0 118 454 5145
Biso mean--22.17 33.84 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074865
X-RAY DIFFRACTIONf_angle_d0.8746667
X-RAY DIFFRACTIONf_dihedral_angle_d12.3132911
X-RAY DIFFRACTIONf_chiral_restr0.056755
X-RAY DIFFRACTIONf_plane_restr0.006912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94420.30321180.22672952307097
1.9442-1.99280.28831270.22473028315598
1.9928-2.04670.2581320.20072994312699
2.0467-2.10690.23411410.190630533194100
2.1069-2.17490.25991270.184530503177100
2.1749-2.25270.21631430.177330323175100
2.2527-2.34280.2321710.172730253196100
2.3428-2.44950.21961490.168130423191100
2.4495-2.57860.22671360.170630733209100
2.5786-2.74010.19831350.166730813216100
2.7401-2.95160.20211310.161830993230100
2.9516-3.24850.21671490.163230813230100
3.2485-3.71840.19551300.145131233253100
3.7184-4.68370.18121380.134431523290100
4.6837-41.35010.19381230.159133203443100
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)
12.59220.4411-2.91141.0971-1.25423.5290.16920.11060.2148-0.2303-0.14850.0867-0.47640.106-0.03940.37070.0484-0.0410.22860.01810.276418.257728.13449.6473
21.60830.6429-0.92752.20420.49091.9990.02120.00460.0909-0.0492-0.0021-0.1219-0.13660.1139-0.00080.0958-0.0057-0.03380.110.01080.156526.213513.822310.0896
32.86744.03461.18126.47790.71495.4608-0.19370.14770.0591-0.66810.242-0.1373-0.35340.0124-0.05650.1903-0.00660.01250.14190.04670.205527.467220.30071.3315
40.99040.121-0.19142.02850.55580.7585-0.04240.11030.02410.0914-0.01760.05110.0418-0.04360.05850.0875-0.0078-0.02610.13020.0060.119421.81963.33329.6468
54.82570.7597-3.28793.4182-0.81154.9656-0.32970.174-0.3957-0.08910.2967-0.49090.50540.19860.10910.1757-0.01230.01670.1446-0.08250.245326.7653-13.79224.7233
60.12010.3156-0.37443.8732-0.08262.2681-0.20040.3732-0.2903-0.11990.0521-0.11420.2484-0.13830.05590.1471-0.03260.02910.146-0.06440.170320.8388-8.28856.2021
75.2459-0.10970.72392.7730.0564.6283-0.05870.2322-0.33760.3642-0.07270.14660.2816-0.17670.11760.1883-0.04190.03680.1179-0.0560.20617.3805-12.33239.0742
80.5151.58491.09365.05313.25372.14490.25610.0147-0.25971.06660.0823-1.10010.25160.0133-0.3390.41550.0226-0.1610.3057-0.03070.377131.7378-11.937514.7508
91.84310.96791.64092.0945-0.72713.5276-0.1069-0.3761-0.23180.6227-0.110.19810.3139-0.02680.1650.3126-0.00230.01730.229-0.01350.18817.5898.171926.9524
101.0478-0.2974-0.29852.31760.92371.44490.0095-0.1496-0.00110.27730.0445-0.16320.06670.1312-0.00710.19260.0132-0.0650.1582-0.01430.142125.879122.389126.9054
114.2578-0.81480.05512.2420.26061.2341-0.149-0.512-0.15060.93840.2674-0.23420.1360.2101-0.03820.43120.0525-0.07430.24490.01370.202126.671615.617835.9039
120.54820.2764-0.17812.13561.03481.1644-0.0173-0.13730.0160.05310.0290.0905-0.14980.06320.00740.16920.0048-0.04630.1556-0.02210.124521.795930.287725.3764
130.41640.39330.39572.38360.88411.6741-0.1115-0.4254-0.27480.59270.1977-0.03070.1650.0827-0.11490.30570.0164-0.07270.2314-0.04620.060625.087932.305936.0434
143.3554-0.07440.53832.75910.92621.81130.0086-0.1860.2863-0.14860.022-0.0671-0.39120.14230.0030.3464-0.0287-0.00290.1762-0.04610.141122.983745.053128.5256
154.38250.335-0.03272.74740.68462.40990.0435-0.06350.2712-0.1448-0.13220.2801-0.46280.02380.09260.40250.0137-0.03060.1657-0.05770.203818.614148.522828.0051
160.2579-0.9618-0.62194.45333.03372.0532-0.03140.14320.0666-1.17440.3368-0.6385-0.09340.2372-0.26520.8172-0.12860.24970.3993-0.06210.491532.894348.905723.3692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A2 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 92 )A36 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 110 )A93 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 214 )A111 - 214
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 235 )A215 - 235
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 266 )A236 - 266
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 288 )A267 - 288
8X-RAY DIFFRACTION8chain 'A' and (resid 289 through 305 )A289 - 305
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 35 )B1 - 35
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 92 )B36 - 92
11X-RAY DIFFRACTION11chain 'B' and (resid 93 through 110 )B93 - 110
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 167 )B111 - 167
13X-RAY DIFFRACTION13chain 'B' and (resid 168 through 189 )B168 - 189
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 266 )B190 - 266
15X-RAY DIFFRACTION15chain 'B' and (resid 267 through 288 )B267 - 288
16X-RAY DIFFRACTION16chain 'B' and (resid 289 through 304 )B289 - 304

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