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- PDB-4p6c: Structure of ribB complexed with inhibitor 4PEH -

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Basic information

Entry
Database: PDB / ID: 4p6c
TitleStructure of ribB complexed with inhibitor 4PEH
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE/LYASE INHIBITOR / ribB / DHBPS / inhibitor / riboflavin / complex / 4PEH / LYASE-LYASE INHIBITOR complex
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
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsIslam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRNWP104, NWP210 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_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_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)51,9854
Polymers51,5232
Non-polymers4622
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-18 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.674, 72.654, 100.085
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: 25761.328 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-RES / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID


Mass: 231.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 1.92 Å3/Da / Density % sol: 35.8 % / Description: Rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: PEG3350, Na2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2010 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→20 Å / Num. obs: 32615 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 14.62 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.7
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 5.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1452)refinement
MAR345dtbdata collection
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57

1g57


Resolution: 1.86→19.62 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1658 5.09 %Random
Rwork0.163 ---
obs0.165 32595 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.4 Å2
Refinement stepCycle: LAST / Resolution: 1.86→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 28 344 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073330
X-RAY DIFFRACTIONf_angle_d1.1414524
X-RAY DIFFRACTIONf_dihedral_angle_d13.8341262
X-RAY DIFFRACTIONf_chiral_restr0.044542
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.863-1.91750.19681350.15792445X-RAY DIFFRACTION96
1.9175-1.97930.23121270.16042542X-RAY DIFFRACTION100
1.9793-2.050.21251410.15672566X-RAY DIFFRACTION100
2.05-2.1320.20721300.1482573X-RAY DIFFRACTION100
2.132-2.22890.22841410.15272546X-RAY DIFFRACTION100
2.2289-2.34620.21561510.16132559X-RAY DIFFRACTION100
2.3462-2.49290.2611460.17522583X-RAY DIFFRACTION100
2.4929-2.6850.2291280.17582574X-RAY DIFFRACTION100
2.685-2.95430.25191310.17682605X-RAY DIFFRACTION100
2.9543-3.380.17831290.16072606X-RAY DIFFRACTION100
3.38-4.25120.1821470.15332632X-RAY DIFFRACTION99
4.2512-19.61730.18171520.16762706X-RAY DIFFRACTION98

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