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- PDB-1vqv: Crystal Structure of Thiamine Monophosphate Kinase (thil) from Aq... -

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Basic information

Entry
Database: PDB / ID: 1vqv
TitleCrystal Structure of Thiamine Monophosphate Kinase (thil) from Aquifex Aeolicus
Componentsthiamine monophosphate kinase
KeywordsTRANSFERASE / THIL / KINASE / DIMER / PHOSPHATE / New York SGX Research Center for Structural Genomics / NYSGXRC / PROTEIN STRUCTURE INITIATIVE / PSI / T1881 / Structural Genomics
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / 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 superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; ...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 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
PHOSPHATE ION / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Thiamine Monophosphate Kinase (Thil) from Aquifex Aeolicus
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionJan 5, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJan 11, 2005ID: 1YAW
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text
Remark 999SEQUENCE The residues GLU 58 (mol A & mol B) and PO4 (1002 & 1004) are refined with alternate ...SEQUENCE The residues GLU 58 (mol A & mol B) and PO4 (1002 & 1004) are refined with alternate conformations. One of the conformations of the side-chain of GLU 58 (mol A and mol B) and PO4 (1002 & 1004) were alternately present at the same position.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thiamine monophosphate kinase
B: thiamine monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7646
Polymers69,3842
Non-polymers3804
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-63 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.580, 65.580, 192.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein thiamine monophosphate kinase


Mass: 34691.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67883, thiamine-phosphate kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium dihydrogen phosphate, Sodium citrate, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 23450 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Rsym value: 0.055 / Net I/σ(I): 21.7
Reflection shellResolution: 2.65→2.74 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL-2000data reduction
SOLVE& SHARPphasing
CNS1.1refinement
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.26 870 -RANDOM
Rwork0.238 ---
obs0.238 22484 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 28 116 4732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009484
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.64105
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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