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- PDB-4p6d: Structure of ribB complexed with PO4 ion -

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Basic information

Entry
Database: PDB / ID: 4p6d
TitleStructure of ribB complexed with PO4 ion
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / ribB / riboflavin / ligand / complex / crystal
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
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 / DHBP synthase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsIslam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC104, BSC210 India
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae.
Authors: Islam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Structure summary
Revision 1.3May 13, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)51,6015
Polymers51,3482
Non-polymers2523
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-21 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.554, 73.597, 95.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25674.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ribB, VC_A1060 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KKP2, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 1.99 Å3/Da / Density % sol: 38.2 % / Description: rod shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaH2PO4, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 / Details: MIRROR
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 52849 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 11.92 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.1
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 7.4 / % possible all: 93.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1615)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57

1g57


Resolution: 1.59→19.436 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2675 5.06 %Random
Rwork0.1688 ---
obs0.1702 52830 96.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 1.59→19.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 14 425 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063134
X-RAY DIFFRACTIONf_angle_d1.0894260
X-RAY DIFFRACTIONf_dihedral_angle_d13.1271198
X-RAY DIFFRACTIONf_chiral_restr0.041511
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.61560.22521040.1692158X-RAY DIFFRACTION80
1.6156-1.64660.19351600.1592676X-RAY DIFFRACTION100
1.6466-1.68020.19681410.15092705X-RAY DIFFRACTION100
1.6802-1.71670.22111570.15342676X-RAY DIFFRACTION100
1.7167-1.75670.18931580.15662690X-RAY DIFFRACTION100
1.7567-1.80060.21481310.16042706X-RAY DIFFRACTION100
1.8006-1.84920.19691320.16562720X-RAY DIFFRACTION100
1.8492-1.90360.24991510.20982383X-RAY DIFFRACTION89
1.9036-1.9650.38871450.2972388X-RAY DIFFRACTION89
1.965-2.03510.19731160.16572734X-RAY DIFFRACTION100
2.0351-2.11650.21370.15822743X-RAY DIFFRACTION100
2.1165-2.21270.18831560.16032684X-RAY DIFFRACTION99
2.2127-2.32920.26221160.2532233X-RAY DIFFRACTION82
2.3292-2.47480.2111370.16972733X-RAY DIFFRACTION100
2.4748-2.66550.17331530.16732750X-RAY DIFFRACTION100
2.6655-2.93290.20661440.16642747X-RAY DIFFRACTION100
2.9329-3.35540.1771610.15892770X-RAY DIFFRACTION100
3.3554-4.22030.13981420.13992734X-RAY DIFFRACTION98
4.2203-19.43760.14441340.13992925X-RAY DIFFRACTION99

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