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- PDB-4jjp: 2.06 Angstrom resolution crystal structure of phosphomethylpyrimi... -

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Basic information

Entry
Database: PDB / ID: 4jjp
Title2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630
ComponentsPhosphomethylpyrimidine kinase
KeywordsTRANSFERASE / IDP05735 / Biosynthesis of cofactors / prosthetic groups / and carriers: Thiamine / phosphomethylpyrimidine kinase / thiD / Clostridium difficile 630 / virulence / pathogenesis / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha/beta fold
Function / homology
Function and homology information


phosphooxymethylpyrimidine kinase / 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
Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.056 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630
Authors: Halavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphomethylpyrimidine kinase
B: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9003
Polymers58,6622
Non-polymers2381
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-13 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.751, 79.741, 92.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphomethylpyrimidine kinase


Mass: 29331.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_15990, thiD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q186F5, phosphooxymethylpyrimidine kinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.79 Å3/Da / Density % sol: 31.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein: 3.7 mg/mL crystallization: 30% Jeffamine ED-2001, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2013 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 26751 / Num. obs: 26751 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1321 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UB0

1ub0


Resolution: 2.056→28.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.056 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21809 1345 5 %RANDOM
Rwork0.18123 ---
obs0.18305 25359 99.34 %-
all-25359 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.432 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å2-0 Å20 Å2
2---0.77 Å2-0 Å2
3---4.01 Å2
Refinement stepCycle: LAST / Resolution: 2.056→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 15 147 3589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223574
X-RAY DIFFRACTIONr_bond_other_d0.0010.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.5712.0134840
X-RAY DIFFRACTIONr_angle_other_deg0.91736040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5215455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32226.471119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47415680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.858154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
X-RAY DIFFRACTIONr_mcbond_it0.7641.52263
X-RAY DIFFRACTIONr_mcbond_other0.1961.5920
X-RAY DIFFRACTIONr_mcangle_it1.39523692
X-RAY DIFFRACTIONr_scbond_it2.27931311
X-RAY DIFFRACTIONr_scangle_it3.7814.51148
LS refinement shellResolution: 2.056→2.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 87 -
Rwork0.252 1718 -
obs-1718 91.62 %
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)
13.90390.431-0.63462.09640.1042.0787-0.05020.10550.0318-0.09290.0324-0.0892-0.01610.04230.01780.08570.0292-0.01510.06220.04020.07919.27094.521327.8089
22.5476-0.7333-0.28253.08740.05361.0910.03210.07470.0122-0.1131-0.07330.0265-0.07920.01020.04120.093-0.0125-0.01190.0790.00660.00325.709814.65920.7478
37.36153.43670.12945.8130.09184.31450.0099-0.47230.5030.2890.04260.2859-0.4808-0.0531-0.05250.19120.04650.03590.1085-0.02760.1324-3.444221.319132.2408
43.8458-1.31660.52985.75881.35044.3958-0.1286-0.42750.09060.3980.2478-0.1443-0.3546-0.0538-0.11920.14240.03210.00720.13140.02250.02153.870410.105838.844
54.57830.3241-0.23652.38050.38812.79-0.0907-0.02560.1465-0.00870.05590.0113-0.0440.04340.03480.06940.0381-0.00470.06440.0050.09128.5374.572132.5932
63.5854-1.0851-0.52642.721-1.46932.0581-0.1014-0.22370.003-0.0179-0.0223-0.17550.23120.02910.12370.1080.00760.01140.1021-0.03520.043940.4999-1.267537.3882
77.5484-1.2545-1.11145.3704-0.98054.1902-0.0768-0.7679-0.74720.1887-0.2822-0.16960.54610.17410.3590.2690.01430.03650.36570.09540.100338.6218-10.974150.1335
86.9784.509-0.139616.2279-0.62417.1823-0.3043-1.571-0.01570.9150.81570.49370.2026-0.1916-0.51140.28170.15850.08310.6660.02390.113926.5114-0.990453.4308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 75
2X-RAY DIFFRACTION2A76 - 178
3X-RAY DIFFRACTION3A179 - 201
4X-RAY DIFFRACTION4A212 - 245
5X-RAY DIFFRACTION5B6 - 74
6X-RAY DIFFRACTION6B75 - 147
7X-RAY DIFFRACTION7B148 - 221
8X-RAY DIFFRACTION8B222 - 243

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