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- PDB-5cc8: Structure of thiamine-monophosphate kinase from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 5cc8
TitleStructure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.75 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 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,10616
Polymers68,7202
Non-polymers1,38614
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-110 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.140, 93.760, 72.490
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-651-

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) / Strain: AB5075-UW / Gene: thiL, HMPREF0021_00055 / Plasmid: AcbaC.17905.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F5HTN4, thiamine-phosphate kinase

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Non-polymers , 5 types, 563 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.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.14 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: native crystal: JCSG+ g10 30% PEG 2000 MME, 150mM KBr; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2; cryo: 20% EG, 5mM Mg/AMPPNP; tray 263060g10, puck ute6-5; iodide crystal: JCSG+ b2: ...Details: native crystal: JCSG+ g10 30% PEG 2000 MME, 150mM KBr; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2; cryo: 20% EG, 5mM Mg/AMPPNP; tray 263060g10, puck ute6-5; iodide crystal: JCSG+ b2: 20% PEG 3350, 200mM NaSCN; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2, AMPPNP; cryo: soak in 10% and 20% of a 2.5M NaI solution in EG added to reservoir solution, 10 sec soaks each; tray 263060b2, puck hmh9-1

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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 18, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 1616237 / Rmerge(I) obs: 0.062 / Χ2: 1.12 / D res high: 2 Å / Num. obs: 76802 / % possible obs: 99.4
ReflectionResolution: 1.75→50 Å / Num. obs: 60460 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.23 % / Biso Wilson estimate: 17.54 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.052 / Χ2: 1.012 / Net I/σ(I): 33.71 / Num. measured all: 861120
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.88.290.8440.5773.8736491854685350.61799.9
1.8-1.840.8930.4423.4437339834683400.50199.9
1.84-1.90.9440.3494.2837849814281360.39399.9
1.9-1.960.9640.2366.4138186787478730.265100
1.96-2.020.9750.2047.4638521761476110.228100
2.02-2.090.9860.15110.3938863738073770.167100
2.09-2.170.9920.12913.644282716971680.142100
2.17-2.260.9950.10618.0548953685168460.11499.9
2.26-2.360.9970.09420.5749949659965940.10199.9
2.36-2.470.9980.0824.0150219625962530.08699.9
2.47-2.610.9980.0727.6151788601460030.07599.8
2.61-2.770.9990.06332.0654025563756320.06799.9
2.77-2.960.9990.05439.560031531553070.05699.8
2.96-3.20.9990.04447.1956713495849550.04699.9
3.2-3.510.03656.2752130455945560.03899.9
3.5-3.9110.03167.3946642409140910.033100
3.91-4.5210.02774.5941578364236340.02999.8
4.52-5.5310.02673.5835237305030490.027100
5.53-7.8310.02768.0527687237423740.028100
7.83-500.9990.02284.114637129612890.02399.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER3.15phasing
ARPmodel building
Cootmodel building
PHENIX(1.10pre_2089: ???)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD
Starting model: iodide soak

Resolution: 1.75→47.905 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3078 5.09 %Random selection
Rwork0.1589 57359 --
obs0.1606 60437 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.4 Å2 / Biso mean: 24.0567 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 1.75→47.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 74 551 5049
Biso mean--15.78 33.15 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064649
X-RAY DIFFRACTIONf_angle_d1.0166373
X-RAY DIFFRACTIONf_chiral_restr0.049741
X-RAY DIFFRACTIONf_plane_restr0.005844
X-RAY DIFFRACTIONf_dihedral_angle_d11.1812792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.77740.21951430.179225502693100
1.7774-1.80650.24491340.18825692703100
1.8065-1.83760.23111290.182825882717100
1.8376-1.87110.23061330.184225662699100
1.8711-1.9070.2211240.177126172741100
1.907-1.9460.22251390.165825692708100
1.946-1.98830.22771340.173226032737100
1.9883-2.03450.1791430.164925702713100
2.0345-2.08540.19751470.163125802727100
2.0854-2.14180.19071380.155725732711100
2.1418-2.20480.21151660.162325542720100
2.2048-2.2760.17341310.160726292760100
2.276-2.35730.20941430.165225742717100
2.3573-2.45170.2121420.163826022744100
2.4517-2.56330.21281570.162625682725100
2.5633-2.69840.20781560.163825992755100
2.6984-2.86750.19961350.166726112746100
2.8675-3.08880.17721360.160326262762100
3.0888-3.39960.17491420.152826292771100
3.3996-3.89130.19681350.140926742809100
3.8913-4.90190.17031520.138426742826100
4.9019-47.9230.15981190.16092834295399
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)
13.7918-2.5584-2.96883.4866-0.38425.5152-0.03350.42560.4637-0.41520.13780.0311-0.3692-0.1206-0.14770.299-0.0135-0.00510.18940.02820.21222.344629.30865.0123
20.23670.1344-0.04511.95070.50661.1384-0.04390.01170.0156-0.14450.0145-0.0164-0.13680.08280.02840.0945-0.018-0.02380.1322-0.00570.109723.279816.19710.7231
37.26181.59160.31122.77380.4552.9693-0.2070.07450.2529-0.54880.1634-0.0373-0.26630.1380.04510.2012-0.0458-0.0020.13430.02870.097627.334320.220.9343
40.245-0.01250.07151.62370.76070.9095-0.0480.04-0.0128-0.02430.04510.0218-0.02520.02720.00430.0602-0.0129-0.01320.1327-0.00230.111222.93845.59337.9857
51.76820.4712-0.31542.89920.75981.8709-0.10120.1625-0.22890.08330.1044-0.18180.21240.03840.01080.1069-0.00850.01270.1084-0.02420.134621.87-8.68548.7326
62.6107-0.58960.31463.85190.09143.54940.00870.0577-0.25980.50740.08680.00730.24760.0978-0.07560.1756-0.0236-0.01240.1148-0.02790.149221.175-15.161810.1185
70.97371.01861.15691.8485-0.3433.4423-0.0623-0.2103-0.06920.4943-0.07830.17340.1797-0.09310.0750.1887-0.00210.02030.149-0.02980.137916.46799.188627.1012
81.969-0.38350.45322.08390.24372.2047-0.0230.01490.01320.2353-0.0218-0.1534-0.02660.15470.06280.1283-0.0074-0.03270.0993-0.01350.103925.80122.67326.3586
96.6637-2.2608-1.00263.60980.52511.7574-0.2112-0.4155-0.13570.69240.2215-0.18950.10740.2051-0.0170.27840.013-0.05890.15280.01350.122526.802916.198635.7116
100.27540.2005-0.0692.31721.04060.80950.04240.00180.01370.096-0.01990.0058-0.06840.0355-0.01760.1477-0.0004-0.01950.1314-0.00370.093623.214331.048628.1759
112.2798-0.06920.25091.9670.44441.86570.0438-0.05630.119-0.1175-0.0254-0.0478-0.31890.0402-0.00270.2536-0.0032-0.00550.0878-0.00880.104123.16345.351927.6421
122.54990.29450.12151.98970.24252.25690.1097-0.05380.3453-0.4383-0.09490.0922-0.33940.0205-0.01160.38210.02950.03110.1346-0.01860.169421.674251.73426.8621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 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 266 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 298 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 3 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 265 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 266 through 298 )B0

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