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- PDB-3enn: 2.1A crystal structure of glucose/ribitol dehydrogenase from bruc... -

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Basic information

Entry
Database: PDB / ID: 3enn
Title2.1A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis (p43212)
ComponentsGLUCOSE/RIBITOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BRUCELLA / MELITENSIS / GLUCOSE / RIBITOL / DEHYDROGENASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.1A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis (p43212)
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: GLUCOSE/RIBITOL DEHYDROGENASE
B: GLUCOSE/RIBITOL DEHYDROGENASE
C: GLUCOSE/RIBITOL DEHYDROGENASE
D: GLUCOSE/RIBITOL DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)105,1454
Polymers105,1454
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-87 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.500, 119.500, 136.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

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Components

#1: Protein
GLUCOSE/RIBITOL DEHYDROGENASE


Mass: 26286.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: BMEI1477, BRUCELLA MELITENSIS / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YFP3, UniProt: Q2YMG6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 45% MPD, 0.1M TRIS pH 8.5, 0.2M AMMONIUM ACETATE, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: SATURN 944 / Detector: CCD / Date: Sep 23, 2008 / Details: MULTI-LAYER OPTICS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 57871 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.1
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.4816.2502024231100
2.15-2.210.3787.9560584117100
2.21-2.280.2949.7549183985100
2.28-2.350.24610.9544613920100
2.35-2.420.20812.3526673757100
2.42-2.510.17214.2516983671100
2.51-2.60.14416.249991352999.9
2.6-2.710.13217.3485553411100
2.71-2.830.11619.3467103277100
2.83-2.970.10221.9450213153100
2.97-3.130.09523.8424202971100
3.13-3.320.08626.3405522845100
3.32-3.550.07729.537874266299.8
3.55-3.830.07630.5355042500100
3.83-4.20.07332.2326352303100
4.2-4.70.07233.829803211799.9
4.7-5.420.07132.826375187599.9
5.42-6.640.07431.1221881603100
6.64-9.390.0734.3170981275100
9.390.06834.3828766988

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.97 Å
Translation3 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Highest resolution: 2.1 Å / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 4.47 / SU ML: 0.121 / SU R Cruickshank DPI: 0.218 / SU Rfree: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2938 5.1 %RANDOM
Rwork0.188 ---
obs0.19 57869 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.54 Å2 / Biso mean: 24.884 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7066 0 0 359 7425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227146
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9629640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65424.11292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.508151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4971556
X-RAY DIFFRACTIONr_chiral_restr0.1010.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025284
X-RAY DIFFRACTIONr_nbd_refined0.210.24494
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2636
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.216
X-RAY DIFFRACTIONr_mcbond_it0.6931.54779
X-RAY DIFFRACTIONr_mcangle_it1.18427440
X-RAY DIFFRACTIONr_scbond_it1.86232581
X-RAY DIFFRACTIONr_scangle_it3.0384.52197
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 210 -
Rwork0.247 4018 -
all-4228 -
obs--99.98 %

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