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- PDB-5cm7: Structure of thiamine-monophosphate kinase from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 5cm7
TitleStructure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / SSGCID / Acinetobacter baumannii / Thiamine-monophosphate kinase / thiamine diphosphate / TPP / adenosine diphosphate / ADP / 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
ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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)70,80918
Polymers68,7202
Non-polymers2,08916
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-216 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 117.120, 55.890
Angle α, β, γ (deg.)90.000, 108.570, 90.000
Int Tables number4
Space group name H-MP1211

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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 / 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, 793 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus E5: 30mM each: Diethylene glycol, Triethylene-glycol, Tetraethylene glycol, Pentaethylene glycol; 100mM Imidazole, MES monohydrate (acid); 20% v/v PEG 500 MME; ...Details: Molecular Dimensions Morpheus E5: 30mM each: Diethylene glycol, Triethylene-glycol, Tetraethylene glycol, Pentaethylene glycol; 100mM Imidazole, MES monohydrate (acid); 20% v/v PEG 500 MME; 10% w/v PEG 20000; AnphA.17905.a.B1.PW37686 at 30mg/ml, 5mM each MgCl2, ADO and TPP; cryo: direct; tray 264490e5, puck ute6-11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 89068 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 10.94 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Χ2: 1.015 / Net I/σ(I): 24.47 / Num. measured all: 991836
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.594.20.8820.3763.5526382660962660.42794.8
1.59-1.630.9410.3455.2445655645864420.37299.8
1.63-1.680.9620.3046.1748853623462320.325100
1.68-1.730.9710.2667.2149616607660760.284100
1.73-1.790.9810.2238.750070586658590.23799.9
1.79-1.850.9860.19510.150554570656940.20799.8
1.85-1.920.9930.15112.8451349553855360.159100
1.92-20.9950.12515.7351027529452840.13299.8
2-2.090.9960.10420.1951136508350800.1199.9
2.09-2.190.9970.09223.5250803484448380.09699.9
2.19-2.310.9980.08128.454658466446490.08599.7
2.31-2.450.9980.07433.8357551436243560.07799.9
2.45-2.620.9990.06837.156950410441000.07199.9
2.62-2.830.9990.06242.157356387238640.06499.8
2.83-3.10.9990.05548.9157533353035250.05699.9
3.1-3.470.9990.04961.9861910317831730.0599.8
3.47-410.04472.0858725282728170.04599.6
4-4.910.0475.4349140238623800.04199.7
4.9-6.9310.04272.2940319187518660.04399.5
6.930.9990.03678.8822249104710310.03798.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cc8

5cc8


Resolution: 1.55→44.501 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 2021 2.27 %
Rwork0.1419 87009 -
obs0.1425 89030 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.66 Å2 / Biso mean: 17.9481 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.55→44.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 118 780 5517
Biso mean--11.24 29.25 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065040
X-RAY DIFFRACTIONf_angle_d1.0856931
X-RAY DIFFRACTIONf_chiral_restr0.05780
X-RAY DIFFRACTIONf_plane_restr0.005952
X-RAY DIFFRACTIONf_dihedral_angle_d11.293082
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 (%)
1.55-1.58880.24031610.19675840600195
1.5888-1.63170.19881510.165162236374100
1.6317-1.67970.1831490.151361906339100
1.6797-1.7340.17911570.148762476404100
1.734-1.79590.17371300.143362336363100
1.7959-1.86780.18311500.146862206370100
1.8678-1.95290.18761370.148162746411100
1.9529-2.05580.18791330.143962056338100
2.0558-2.18460.17111330.140462386371100
2.1846-2.35330.17091200.143362606380100
2.3533-2.59010.17161730.14162216394100
2.5901-2.96480.1551470.145162786425100
2.9648-3.7350.12931260.133862636389100
3.735-44.51920.15441540.127163176471100
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)
11.5203-0.44230.12521.858-0.51260.12220.03930.076-0.0023-0.0827-0.041-0.18590.04550.08760.01320.103-0.00220.00120.1151-0.00510.112655.96016.756861.3425
20.8894-0.00910.24241.1196-0.11620.79820.0036-0.0286-0.0680.10960.0094-0.08240.03320.0209-0.01980.0689-0.004-0.00030.07420.00820.076843.7445-4.405163.3238
32.365-0.59140.78752.7978-0.98833.49420.00790.1151-0.16270.09470.0134-0.2253-0.00520.1998-0.01990.05830.00190.00790.0966-0.01940.141154.2839-7.445760.9505
40.5720.34260.25350.590.22820.28680.00840.0534-0.00840.04530.009-0.03540.01370.015-0.01350.06480.00290.01110.08230.01040.063837.9758-6.829656.8684
50.95640.14970.3431.8430.01290.48660.0250.1276-0.0001-0.0547-0.03780.05130.02080.04120.00480.05050.00010.01820.0876-0.00940.052525.0254-13.139551.1552
60.06330.27750.14361.32120.62640.30630.3236-0.35390.12760.4926-0.24560.08840.3441-0.0983-0.0560.2209-0.08170.06150.2888-0.05120.162320.7937-17.114862.2024
71.5590.3252-1.0540.2836-0.91962.82540.1261-0.15610.14530.21-0.04960.2846-0.1779-0.2599-0.10370.1126-0.00590.02150.1411-0.02320.155129.51589.240464.8604
80.82610.2825-0.07130.96770.03291.14110.0302-0.1460.02110.1127-0.05190.07390.13-0.07470.01380.0896-0.01420.00390.0815-0.00080.066841.981410.328475.1152
91.65120.7835-0.58493.0826-1.55262.24410.0134-0.25120.09410.183-0.04930.29850.0468-0.25410.00610.1108-0.01320.04120.169-0.03650.11831.738512.281179.0933
100.54290.32150.3460.78630.25280.84180.0343-0.080.03620.1357-0.087-0.0316-0.0074-0.01750.03890.09020.0025-0.00320.0760.00220.090547.729217.243976.2251
110.6834-0.09040.16560.9690.37851.7243-0.0068-0.00650.09840.11770.0271-0.1203-0.05730.1650.02290.1078-0.0221-0.0380.10060.00020.133360.350624.715979.1777
120.73131.17550.74851.87151.20650.78440.236-0.0254-0.24780.51730.0967-0.65660.20010.1665-0.22980.2778-0.0126-0.12220.3105-0.00110.333566.235514.958584.8874
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 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 110 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 189 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 288 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 305 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 35 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 92 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 110 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 189 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 288 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 289 through 305 )B0

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