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- PDB-4yl5: Structure of a putative phosphomethylpyrimidine kinase from Acine... -

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Basic information

Entry
Database: PDB / ID: 4yl5
TitleStructure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii
ComponentsPutative phosphomethylpyrimidine kinase
KeywordsTRANSFERASE / putative phosphomethylpyrimidine kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / thiamine biosynthetic process
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative phosphomethylpyrimidine kinase / :
Similarity search - Component
Biological speciesAcinetobacter baumannii IS-123 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochemistry / Year: 2024
Title: Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate.
Authors: De Vitto, H. / Belfon, K.K.J. / Sharma, N. / Toay, S. / Abendroth, J. / Dranow, D.M. / Lukacs, C.M. / Choi, R. / Udell, H.S. / Willis, S. / Barrera, G. / Beyer, O. / Li, T.D. / Hicks, K.A. / ...Authors: De Vitto, H. / Belfon, K.K.J. / Sharma, N. / Toay, S. / Abendroth, J. / Dranow, D.M. / Lukacs, C.M. / Choi, R. / Udell, H.S. / Willis, S. / Barrera, G. / Beyer, O. / Li, T.D. / Hicks, K.A. / Torelli, A.T. / French, J.B.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8553
Polymers27,7311
Non-polymers1242
Water3,351186
1
A: Putative phosphomethylpyrimidine kinase
hetero molecules

A: Putative phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7096
Polymers55,4612
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3200 Å2
ΔGint-4 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 108.100, 88.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-415-

HOH

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Components

#1: Protein Putative phosphomethylpyrimidine kinase /


Mass: 27730.598 Da / Num. of mol.: 1 / Fragment: UNP residues 2-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii IS-123 (bacteria)
Gene: ACINIS123_0279 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J5A2R3, UniProt: A0A0J9X285*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytics MGSC1 screen, c8: 25% PEG 4000, 200mM ammonium citrate, 100mM Na citrate/HCl, pH 5.6; AcbaC.00867.a.B1.PW37632 at 22 mg/ml, tray 261062, puck pma4-8; cryo: 20% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 26, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31564 / Num. obs: 31307 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21.2 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.042 / Χ2: 1.006 / Net I/σ(I): 23.94 / Num. measured all: 141847
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
1.7-1.743.80.7830.4092.396037233621620.592.6
1.74-1.790.8770.3263.457123220821550.38697.6
1.79-1.840.9290.2834.658732219921980.326100
1.84-1.90.9670.2036.999277212421240.23100
1.9-1.960.9820.1699.110102206020590.189100
1.96-2.030.9870.13811.119901200219990.15499.9
2.03-2.110.9940.09915.149499192819280.111100
2.11-2.190.9960.07718.789137185218520.086100
2.19-2.290.9970.06322.218787178917870.07199.9
2.29-2.40.9980.05226.188448170417040.059100
2.4-2.530.9980.04430.78023162716230.0599.8
2.53-2.690.9980.0433.817595154615450.04599.9
2.69-2.870.9990.03438.437081143714370.039100
2.87-3.10.9990.02944.036758138013800.033100
3.1-3.40.9990.02650.596061124712470.03100
3.4-3.80.9990.02354.865539114911490.026100
3.8-4.390.9990.02160.594848100910080.02399.9
4.39-5.3810.01862.241438698680.0299.9
5.38-7.610.01958.2831796936930.021100
7.60.9990.01659.315774053890.01896

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.32 Å46.18 Å
Translation4.32 Å46.18 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
BALBESphasing
PHASERphasing
PHENIX(phenix.refine: dev_1965)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4c51

4c51


Resolution: 1.7→29.41 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 1647 5.26 %Random selection
Rwork0.16 29647 --
obs0.1609 31294 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.33 Å2 / Biso mean: 28.5359 Å2 / Biso min: 12.77 Å2
Refinement stepCycle: final / Resolution: 1.7→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 8 187 1829
Biso mean--33.29 39.13 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071716
X-RAY DIFFRACTIONf_angle_d1.0712349
X-RAY DIFFRACTIONf_chiral_restr0.056289
X-RAY DIFFRACTIONf_plane_restr0.005306
X-RAY DIFFRACTIONf_dihedral_angle_d13.333614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.26551430.24152286242993
1.75-1.80650.26121410.21032398253998
1.8065-1.87110.21431330.191424602593100
1.8711-1.9460.19561460.170524422588100
1.946-2.03450.23041520.173224602612100
2.0345-2.14180.17771510.159224392590100
2.1418-2.27590.16531330.159424982631100
2.2759-2.45150.16211240.145724922616100
2.4515-2.69810.16141300.155424912621100
2.6981-3.08820.19431240.164325242648100
3.0882-3.88930.1651340.152225332667100
3.8893-29.41440.14971360.14862624276099
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)
12.42770.28140.40031.91360.33082.91530.1099-0.0238-0.0059-0.0033-0.0157-0.01190.03760.0206-0.07750.12080.0061-0.00040.1132-0.00010.10642.155931.781328.1272
22.29720.0695-1.37281.11950.58152.74980.044-0.0812-0.06270.1295-0.00750.03580.2406-0.0355-0.02530.1715-0.0169-0.02320.14260.02210.14020.745229.192642.2032
33.6826-2.0161.20017.9536-3.26075.75630.1158-0.45380.27880.46740.17280.6173-0.4347-0.3677-0.25580.2738-0.07150.04920.2379-0.04890.2536-4.737239.858151.0933
47.3883-1.7834-1.46369.5378-0.40955.1830.2076-0.37430.54840.4287-0.19710.5637-0.3779-0.6329-0.03760.2522-0.04750.06410.2017-0.06540.3502-1.855346.019947.533
52.77370.37941.12851.19720.77363.9002-0.0307-0.19240.4488-0.0510.02030.0238-0.2475-0.0670.02990.2102-0.04280.04150.1342-0.0590.21323.815348.60637.5943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:90 )A9 - 90
2X-RAY DIFFRACTION2( CHAIN A AND RESID 91:158 )A91 - 158
3X-RAY DIFFRACTION3( CHAIN A AND RESID 159:186 )A159 - 186
4X-RAY DIFFRACTION4( CHAIN A AND RESID 187:217 )A187 - 217
5X-RAY DIFFRACTION5( CHAIN A AND RESID 218:245 )A218 - 245

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