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- PDB-3mcq: Crystal structure of Thiamine-monophosphate kinase (Mfla_0573) fr... -

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Basic information

Entry
Database: PDB / ID: 3mcq
TitleCrystal structure of Thiamine-monophosphate kinase (Mfla_0573) from METHYLOBACILLUS FLAGELLATUS KT at 1.91 A resolution
ComponentsThiamine-monophosphate kinase
KeywordsTRANSFERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesMethylobacillus flagellatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Thiamine-monophosphate kinase (Mfla_0573) from METHYLOBACILLUS FLAGELLATUS KT at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_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_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

Downloads & links

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Assembly

Deposited unit
A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,65411
Polymers34,4511
Non-polymers1,20310
Water2,450136
1
A: Thiamine-monophosphate kinase
hetero molecules

A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,30822
Polymers68,9022
Non-polymers2,40720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area10400 Å2
ΔGint-51 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.225, 59.225, 159.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A DIMER IS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiamine-monophosphate kinase


Mass: 34450.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus (bacteria) / Strain: KT / ATCC 51484 / DSM 6875 / Gene: Mfla_0573 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1H3U4, thiamine-phosphate kinase

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Non-polymers , 6 types, 146 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE THIS CONSTRUCT (1-318) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THIS CONSTRUCT (1-318) WAS EXPRESSED WITH THE 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: 2.35 Å3/Da / Density % sol: 47.61 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5.0000% polyethylene glycol 3000, 44.0000% polyethylene glycol 400, 0.1M MES pH 6.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97951,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / 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
20.979511
30.979361
ReflectionResolution: 1.91→29.117 Å / Num. obs: 25856 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.156 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.642.3188564918199.1
1.98-2.060.4783.4203194794199.3
2.06-2.150.4144.8243584646199.4
2.15-2.260.2787.2271774711199.1
2.26-2.410.20410.3343185103199.2
2.41-2.590.14514.7360234675199.3
2.59-2.850.09320.5374434856199.5
2.85-3.260.05530.8371784838199.6
3.26-4.10.03844.6368194832199.6
4.1-29.1170.0352368694919199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→29.117 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 8.429 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. POLYETHYLENE GLYCOL (PEG, PGE, PG4, AND 1PE) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. SODIUM IONS (NA) FROM THE PROTEIN BUFFER HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 6. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1315 5.1 %RANDOM
Rwork0.197 ---
obs0.198 25833 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 23.992 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 78 136 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222452
X-RAY DIFFRACTIONr_bond_other_d0.0030.021649
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9783339
X-RAY DIFFRACTIONr_angle_other_deg1.25134066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9524.74799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3211513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
X-RAY DIFFRACTIONr_mcbond_it0.6671.51548
X-RAY DIFFRACTIONr_mcbond_other0.181.5628
X-RAY DIFFRACTIONr_mcangle_it1.19622493
X-RAY DIFFRACTIONr_scbond_it2.1853904
X-RAY DIFFRACTIONr_scangle_it3.5744.5830
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 96 -
Rwork0.29 1743 -
all-1839 -
obs--99.14 %
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)
10.7776-0.02110.12460.8958-0.52452.6792-0.02340.087-0.064-0.08780.0321-0.0440.14340.0408-0.00870.20810.0050.01080.05010.01040.029825.667-1.02845.822
23.134-0.72971.67721.9847-1.52523.5946-0.36250.04760.16160.57190.1521-0.1248-1.01860.0990.21040.5878-0.0394-0.03690.07870.03260.045827.45723.44538.673
310.2114-0.68379.75860.15410.820935.9984-0.1007-0.74561.3705-0.08530.0973-0.0636-0.8907-1.21250.00350.99660.1308-0.19220.26910.10990.644621.54437.98742.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 141
2X-RAY DIFFRACTION2A142 - 296
3X-RAY DIFFRACTION3A297 - 308

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