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- PDB-2o7p: The crystal structure of RibD from Escherichia coli in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2o7p
TitleThe crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain
ComponentsRiboflavin biosynthesis protein ribD
KeywordsHYDROLASE / OXIDOREDUCTASE / NADP+ complex / alpha and beta class with mainly parallell beta strands / Structural Genomics / HTP-protein Escherichia coli / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding / zinc ion binding
Similarity search - Function
Riboflavin biosynthesis protein RibD / Riboflavin-specific deaminase, C-terminal / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. ...Riboflavin biosynthesis protein RibD / Riboflavin-specific deaminase, C-terminal / : / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Riboflavin biosynthesis protein RibD / Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMoche, M. / Stenmark, P. / Gurmu, D. / Nordlund, P. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism.
Authors: Stenmark, P. / Moche, M. / Gurmu, D. / Nordlund, P.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Riboflavin biosynthesis protein ribD
B: Riboflavin biosynthesis protein ribD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2334
Polymers84,7462
Non-polymers1,4872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.000, 173.000, 77.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains the biological unit of RibD

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Components

#1: Protein Riboflavin biosynthesis protein ribD


Mass: 42372.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PT73.3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P25539, UniProt: Q3ZUB0*PLUS, diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Has protein modificationY

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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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) at pH 7.4, 150mM NaCl, 10mM mercaptoethanol, 10% (v/v) glycerol, 2mM EDTA, 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR ...Details: 20mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) at pH 7.4, 150mM NaCl, 10mM mercaptoethanol, 10% (v/v) glycerol, 2mM EDTA, 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2836 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2836 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 27098 / Num. obs: 27042 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2514 / Rsym value: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G6V

2g6v


Resolution: 3→28.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 37.106 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.804 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 1359 5 %RANDOM
Rwork0.2122 ---
all0.21496 27057 --
obs0.21496 25679 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.52 Å20 Å2
2---1.03 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 3→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 96 0 5523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225633
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9837667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.87623.817241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.21115914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0711544
X-RAY DIFFRACTIONr_chiral_restr0.1110.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024224
X-RAY DIFFRACTIONr_nbd_refined0.2470.22424
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.24
X-RAY DIFFRACTIONr_mcbond_it0.8661.53612
X-RAY DIFFRACTIONr_mcangle_it1.38725638
X-RAY DIFFRACTIONr_scbond_it1.82332278
X-RAY DIFFRACTIONr_scangle_it3.0444.52029
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 98 -
Rwork0.285 1857 -
obs-1857 100 %

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