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- PDB-3dzv: Crystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinas... -

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Basic information

Entry
Database: PDB / ID: 3dzv
TitleCrystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinase (NP_816404.1) from ENTEROCOCCUS FAECALIS V583 at 2.57 A resolution
Components4-methyl-5-(beta-hydroxyethyl)thiazole kinase
KeywordsTRANSFERASE / NP_816404.1 / 4-methyl-5-(beta-hydroxyethyl)thiazole kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / ATP-binding / Kinase / Nucleotide-binding / Thiamine biosynthesis / Hydroxyethylthiazole kinase family
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinase (NP_816404.1) from ENTEROCOCCUS FAECALIS V583 at 2.57 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
B: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4978
Polymers60,2582
Non-polymers1,2396
Water2,234124
1
A: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules

A: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules

A: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24612
Polymers90,3883
Non-polymers1,8589
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9960 Å2
ΔGint-153 kcal/mol
Surface area28170 Å2
MethodPISA
2
B: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules

B: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules

B: 4-methyl-5-(beta-hydroxyethyl)thiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24612
Polymers90,3883
Non-polymers1,8589
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10080 Å2
ΔGint-158 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.705, 181.705, 181.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-273-

SO4

21A-273-

SO4

31B-273-

SO4

41B-273-

SO4

51A-501-

HOH

61A-569-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEVAL4AA1 - 52 - 6
21MSEVAL4BB1 - 52 - 6
32LYSLEU2AA6 - 2727 - 273
42LYSLEU2BB6 - 2727 - 273

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Components

#1: Protein 4-methyl-5-(beta-hydroxyethyl)thiazole kinase


Mass: 30129.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: NP_816404.1, EF_2777 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q830K4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.6M ammonium sulfate, 0.1M citric acid pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97954,0.97968
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979541
30.979681
ReflectionResolution: 2.57→29.476 Å / Num. obs: 31815 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 50.24 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.57-2.645.60.9761.61311023350.976100
2.64-2.715.60.8681.81281622780.868100
2.71-2.795.60.7382.11248122170.738100
2.79-2.875.60.6052.61204621420.605100
2.87-2.975.60.542.91177420870.54100
2.97-3.075.60.4153.91135020170.415100
3.07-3.195.60.3364.91095119490.336100
3.19-3.325.60.2496.81057718760.249100
3.32-3.475.60.2058.71023418230.205100
3.47-3.635.60.15611.2963917220.156100
3.63-3.835.60.14813.1917916410.148100
3.83-4.065.60.12915.5857915420.129100
4.06-4.345.60.10718.3821414660.107100
4.34-4.695.60.08722.2757813640.087100
4.69-5.145.60.07922.7714112850.079100
5.14-5.755.60.09318.9629411320.093100
5.75-6.645.50.09319.5565910220.093100
6.64-8.135.50.06825.547548700.068100
8.13-11.495.40.04632.636676790.046100
11.49-29.485.10.0530.918723680.0594.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.57→29.476 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.667 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.2
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ADP IS MODELED BASED ON DENSITY, THE CRYSTAL WAS OBTAINED IN PRESENCE OF 1 mM ATP. SO4 MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1604 5 %RANDOM
Rwork0.175 ---
obs0.177 31794 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.195 Å2
Refinement stepCycle: LAST / Resolution: 2.57→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 74 124 4227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224161
X-RAY DIFFRACTIONr_bond_other_d0.0020.022657
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.995668
X-RAY DIFFRACTIONr_angle_other_deg0.93136574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.14626.158177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55315702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7291515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
X-RAY DIFFRACTIONr_nbd_refined0.2230.2931
X-RAY DIFFRACTIONr_nbd_other0.1870.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22069
X-RAY DIFFRACTIONr_nbtor_other0.0880.22146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it1.63332839
X-RAY DIFFRACTIONr_mcbond_other0.24831070
X-RAY DIFFRACTIONr_mcangle_it2.58254261
X-RAY DIFFRACTIONr_scbond_it5.26181624
X-RAY DIFFRACTIONr_scangle_it7.324111405
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1537TIGHT POSITIONAL0.050.07
1760MEDIUM POSITIONAL0.180.2
1537TIGHT THERMAL0.110.5
1760MEDIUM THERMAL0.351
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 122 -
Rwork0.297 2196 -
all-2318 -
obs--99.27 %

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