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- PDB-1snn: 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus ... -

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Basic information

Entry
Database: PDB / ID: 1snn
Title3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsISOMERASE / riboflavin biosynthesis
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsSteinbacher, S. / Schiffmann, S. / Huber, R. / Bacher, A. / Fischer, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate.
Authors: Steinbacher, S. / Schiffmann, S. / Bacher, A. / Fischer, M.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism
Authors: Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M.
History
DepositionMar 11, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,38011
Polymers51,5632
Non-polymers8179
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-170 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.395, 69.366, 57.574
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is identical to the assymmetric dimer

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 25781.553 Da / Num. of mol.: 2 / Mutation: H147S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0055 / Plasmid: PNCO-MJ / Production host: Escherichia coli (E. coli) / Strain (production host): XL1
References: UniProt: Q60364, Isomerases; Intramolecular transferases; Transferring other groups
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE / Ribulose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 1.97 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.283, 1.2823
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2831
21.28231
ReflectionResolution: 1.55→20 Å / Num. all: 53846 / Num. obs: 53846 / % possible obs: 0.883 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.5
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2 / % possible all: 92.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PVY

1pvy


Resolution: 1.55→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The purpose of the present study was to unumbiguously identify a metal ion as zinc. Therefore a data set including the anomlaous data was collected at the zinc absorption edge. The structure ...Details: The purpose of the present study was to unumbiguously identify a metal ion as zinc. Therefore a data set including the anomlaous data was collected at the zinc absorption edge. The structure is virtually identical to the entry 1PVY. Therefore, a simple refinement was sufficient to "solve" the structure. The strcuture was refined against the data set, not containing the anomalous data.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2723 -random
Rwork0.2 ---
all0.21 53820 --
obs0.21 53820 88.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.708 Å20 Å21.218 Å2
2--4.762 Å20 Å2
3----8.47 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 35 352 3857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0105
X-RAY DIFFRACTIONc_angle_deg1.48

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