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- PDB-2g6v: The crystal structure of ribD from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2g6v
TitleThe crystal structure of ribD from Escherichia coli
ComponentsRiboflavin biosynthesis protein ribDRiboflavin
KeywordsHYDROLASE / OXIDOREDUCTASE / ribD apo structure / Structural Genomics / 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. / Cytidine and deoxycytidylate deaminase domain ...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
Riboflavin biosynthesis protein RibD / Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsStenmark, P. / Moche, M. / 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
DepositionFeb 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)89,5992
Polymers89,5992
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-27 kcal/mol
Surface area30870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)172.600, 172.600, 76.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Riboflavin biosynthesis protein ribD / Riboflavin


Mass: 44799.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ribD, ribG / 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, 5-amino-6-(5-phosphoribosylamino)uracil reductase, diaminohydroxyphosphoribosylaminopyrimidine deaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: In 500uL reservoir: 0.1M MES, 3% (v/v) 1,6 Hexandiol, 2+2uL drops , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→28.25 Å / Num. obs: 40482 / % possible obs: 86.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.7 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→28.25 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.906 / SU B: 24.334 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28544 2010 5 %RANDOM
Rwork0.24422 ---
all0.24626 ---
obs0.24626 40426 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 87.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 0 65 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225572
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9617569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28223.817241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.91315916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0571544
X-RAY DIFFRACTIONr_chiral_restr0.0880.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024227
X-RAY DIFFRACTIONr_nbd_refined0.2390.22796
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.211
X-RAY DIFFRACTIONr_mcbond_it0.5341.53656
X-RAY DIFFRACTIONr_mcangle_it0.88225701
X-RAY DIFFRACTIONr_scbond_it1.32332147
X-RAY DIFFRACTIONr_scangle_it2.1134.51868
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 131 -
Rwork0.32 2816 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.6786-2.40723.93371.8884-1.474.94680.49630.9565-0.667-0.6672-0.4656-0.04790.65050.3387-0.0307-0.17190.15240.0536-0.2354-0.0542-0.154442.338544.8931-2.6863
20.9106-0.32840.28787.523-2.91142.84110.024-0.17040.11360.616-0.1083-0.2337-0.25970.12650.0843-0.39080.06450.0134-0.23560.0648-0.261459.778248.943923.0397
36.9749-4.99964.4434.9856-2.11624.93-0.1934-0.89910.03640.54280.39680.3997-0.8318-1.1738-0.20350.0850.19990.18440.0840.0127-0.189847.023104.397917.2068
43.40461.2168-0.01235.91191.86522.5642-0.0248-0.4881-0.00060.68310.1723-0.55340.010.3447-0.1476-0.24810.0461-0.0425-0.1054-0.0716-0.308672.553785.373521.0268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 145
2X-RAY DIFFRACTION1A-4 - -1
3X-RAY DIFFRACTION2A146 - 367
4X-RAY DIFFRACTION3B0 - 145
5X-RAY DIFFRACTION3B-4 - -1
6X-RAY DIFFRACTION4B146 - 367

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