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- PDB-3ix1: Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine bin... -

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Basic information

Entry
Database: PDB / ID: 3ix1
TitlePeriplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein from Bacillus halodurans
ComponentsN-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
KeywordsBIOSYNTHETIC PROTEIN / Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein / Thiamine biosynthesis
Function / homology
Function and homology information


thiamine biosynthetic process / thiamine diphosphate biosynthetic process / plasma membrane
Similarity search - Function
NMT1/THI5 family / SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NFM / Formylaminopyrimidine-binding protein
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBale, S. / Rajashankar, K.R. / Perry, K. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: HMP Binding Protein ThiY and HMP-P Synthase THI5 Are Structural Homologues.
Authors: Bale, S. / Rajashankar, K.R. / Perry, K. / Begley, T.P. / Ealick, S.E.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
B: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9444
Polymers66,6122
Non-polymers3322
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4722
Polymers33,3061
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4722
Polymers33,3061
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.918, 96.953, 104.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein / Thiamine biosynthesis protein


Mass: 33305.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: BH2682 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9K9G5
#2: Chemical ChemComp-NFM / N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide


Mass: 166.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3.0 M NaCl, 100 mM Sodium acetate, 100 mM Li2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 38830 / Num. obs: 23837 / % possible obs: 96.5 % / Redundancy: 4 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Χ2: 1.205 / Net I/σ(I): 4.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2120 / Rsym value: 0.422 / Χ2: 0.699 / % possible all: 87.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→35.47 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 28822 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3712 9.6 %RANDOM
Rwork0.203 ---
all0.203 23837 --
obs0.203 23837 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.202 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 55.01 Å2 / Biso mean: 21.791 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--7.54 Å20 Å20 Å2
2--14.13 Å20 Å2
3----6.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 24 259 4931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 462 9.4 %
Rwork0.277 4462 -
all-4924 -
obs-2120 64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2nfp.paramnfp.top
X-RAY DIFFRACTION3water.param

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