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- PDB-3emk: 2.5A crystal structure of glucose/ribitol dehydrogenase from bruc... -

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Basic information

Entry
Database: PDB / ID: 3emk
Title2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis
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 (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / NAD binding / fatty acid biosynthetic process
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-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: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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

Downloads & links

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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)104,3004
Polymers104,3004
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-93 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.489, 147.939, 63.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
GLUCOSE/RIBITOL DEHYDROGENASE / SHORT-CHAIN DEHYDROGENASE


Mass: 26074.951 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 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YFP3, UniProt: Q2YMG6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.15M DL MALIC ACID, pH 7.0, 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: Jan 1, 2008 / Details: MULTI-LAYER OPTICS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31770 / % possible obs: 94.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.978
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.5-2.592.80.57195.8
2.59-2.6930.48396.6
2.69-2.823.40.45695.5
2.82-2.963.50.34395.2
2.96-3.153.50.26593.9
3.15-3.393.40.16593.1
3.39-3.733.40.11592.5
3.73-4.273.40.09192.5
4.27-5.383.50.07396
5.38-504.30.06497.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.18 Å
Translation2.5 Å44.18 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.04 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 1.114 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1598 5 %RANDOM
Rwork0.20063 ---
obs0.20407 30103 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.237 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2--2.16 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 0 0 130 7138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9629545
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36824.089291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.662151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2381556
X-RAY DIFFRACTIONr_chiral_restr0.1060.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24829
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.61.54756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05327363
X-RAY DIFFRACTIONr_scbond_it1.58432561
X-RAY DIFFRACTIONr_scangle_it2.6134.52182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 113 -
Rwork0.28 2208 -
obs--94.93 %

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