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- PDB-5dd7: Structure of thiamine-monophosphate kinase from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 5dd7
TitleStructure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP and thiamine-monophosphate
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 diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / THIAMIN PHOSPHATE / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 27, 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
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

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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)72,17622
Polymers69,9192
Non-polymers2,25620
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-108 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.960, 93.290, 73.480
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-616-

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: 34959.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: thiL, ABUW_0092 / Plasmid: AcbaC.17905.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5YC82, thiamine-phosphate kinase

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Non-polymers , 6 types, 513 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O4PS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MGCS G4 optimization screen: 19% PEG 3350, 200mM KNa-tartrate, 100mM HEPES/NaOH pH 7.75; AcbaC.17905.a.B1.PW37686 at 30mg/ml with 5mM MgCl2/ANP, then over night soak with in ...Details: Microlytic MGCS G4 optimization screen: 19% PEG 3350, 200mM KNa-tartrate, 100mM HEPES/NaOH pH 7.75; AcbaC.17905.a.B1.PW37686 at 30mg/ml with 5mM MgCl2/ANP, then over night soak with in reservoir solution with 5mM MgCl2/ANP/TMP; cryo: soak solution with 20% EG; tray 264486e7, puck RUX3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 7, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 66411 / Num. obs: 66088 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 18.91 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 0.95 / Net I/σ(I): 22.56 / Num. measured all: 407322
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.746.20.8710.5873.4329982486448240.6499.2
1.74-1.790.920.4684.329114471946690.5198.9
1.79-1.840.9470.3745.3128295457745480.40899.4
1.84-1.90.9660.2817.0927707448444520.30699.3
1.9-1.960.9770.2218.8126907433943150.24199.4
1.96-2.030.9860.17310.8925939419741690.18999.3
2.03-2.110.9920.13413.6725263407240590.14699.7
2.11-2.190.9940.10716.4524263391838960.11799.4
2.19-2.290.9960.08819.5523232375237380.09699.6
2.29-2.40.9970.07622.3522170357735680.08399.7
2.4-2.530.9970.06225.9121359345234460.06899.8
2.53-2.690.9990.05329.5919884321332080.05899.8
2.69-2.870.9990.0443418876307030670.04999.9
2.87-3.10.9990.03740.6817608287628740.0499.9
3.1-3.40.9990.0348.2115980263426320.03399.9
3.4-3.80.9990.02656.0914550241224100.02899.9
3.8-4.390.9990.02460.1212802214721460.026100
4.39-5.3810.02161.7410696180718040.02399.8
5.38-7.610.02258.598362144614430.02499.8
7.60.9990.01961.2743338558200.02195.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.10_2139: ???)phasing
Cootmodel building
PHENIX(1.10_2139: ???)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d9u

5d9u
PDB Unreleased entry


Resolution: 1.7→39.41 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 2015 3.05 %Random selection
Rwork0.1495 64055 --
obs0.1504 66070 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.83 Å2 / Biso mean: 26.7195 Å2 / Biso min: 10.37 Å2
Refinement stepCycle: final / Resolution: 1.7→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 128 496 5232
Biso mean--18.55 34.14 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064912
X-RAY DIFFRACTIONf_angle_d0.8376727
X-RAY DIFFRACTIONf_chiral_restr0.055758
X-RAY DIFFRACTIONf_plane_restr0.006921
X-RAY DIFFRACTIONf_dihedral_angle_d11.372953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.22941370.18924496463399
1.7425-1.78960.271400.18044477461799
1.7896-1.84230.20841530.17574509466299
1.8423-1.90180.21391440.15954501464599
1.9018-1.96970.16471350.15645364671100
1.9697-2.04860.17981420.15374545468799
2.0486-2.14180.17741350.148945274662100
2.1418-2.25470.21441270.147545794706100
2.2547-2.3960.16741390.148645664705100
2.396-2.58090.18141420.153146074749100
2.5809-2.84060.18481590.153845934752100
2.8406-3.25150.17531650.154546014766100
3.2515-4.09580.1641550.136846864841100
4.0958-39.42040.15041420.13844832497499
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)
12.53710.7926-2.64732.562-1.35092.925-0.10960.36090.1971-0.45540.00470.1684-0.2196-0.17840.07380.24830.0259-0.04460.17240.00230.17518.60728.14869.4203
20.5170.0003-0.09511.90140.83121.1663-0.0250.07980.0221-0.0264-0.01520.0294-0.0282-0.0090.02560.0707-0.0106-0.02620.12880.00120.110923.78388.38678.9356
32.450.7076-0.32532.87950.56722.1587-0.15860.2291-0.3440.13030.0477-0.01440.4001-0.10540.08860.1766-0.02570.02150.1442-0.04990.180721.2786-10.98846.8132
40.31830.96250.77032.92762.33851.86220.37520.1202-0.47061.20720.1432-1.05120.6270.1418-0.46970.43790.0648-0.17580.2407-0.03210.416131.755-11.856315.0637
51.4534-0.6041.22513.0739-0.71823.0565-0.1506-0.3022-0.10620.6739-0.06670.25360.1617-0.12650.1540.2612-0.03060.01940.1886-0.02060.1717.37118.287426.9498
60.47430.0166-0.15982.21270.99921.16380.0292-0.06770.02030.207-0.0318-0.0387-0.04280.03680.01620.1637-0.0054-0.03660.1325-0.01010.112623.864527.371428.0625
71.55490.33170.24643.5721.68132.0408-0.0404-0.18170.26280.04720.1007-0.3489-0.50640.1901-0.03570.3232-0.03290.01160.2007-0.06420.260727.783549.553832.3648
82.7519-0.2939-0.02773.0785-0.02371.64810.0541-0.11490.3197-0.1019-0.0733-0.0011-0.4353-0.08130.00880.33560.0183-0.03370.1504-0.05810.177120.183646.241929.1973
90.21040.5380.49131.38551.35511.6130.3503-0.07350.2801-1.01410.3214-1.1827-0.70440.2501-0.64280.5797-0.09760.16360.2499-0.04480.411233.14747.663422.4321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 214 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 288 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 305 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 35 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 214 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 215 through 235 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 236 through 288 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 289 through 305 )B0

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