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- PDB-3grk: Crystal structure of short chain dehydrogenase reductase SDR gluc... -

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Basic information

Entry
Database: PDB / ID: 3grk
TitleCrystal structure of short chain dehydrogenase reductase SDR glucose-ribitol dehydrogenase from Brucella melitensis
ComponentsEnoyl-(acyl-carrier-protein) reductase (NADH)
KeywordsOXIDOREDUCTASE / SSGCID / NIAID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / 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
Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of short chain dehydrogenase reductase SDR glucose-ribitol dehydrogenase from Brucella melitensis
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-(acyl-carrier-protein) reductase (NADH)
B: Enoyl-(acyl-carrier-protein) reductase (NADH)
C: Enoyl-(acyl-carrier-protein) reductase (NADH)
D: Enoyl-(acyl-carrier-protein) reductase (NADH)
E: Enoyl-(acyl-carrier-protein) reductase (NADH)
F: Enoyl-(acyl-carrier-protein) reductase (NADH)
G: Enoyl-(acyl-carrier-protein) reductase (NADH)
H: Enoyl-(acyl-carrier-protein) reductase (NADH)


Theoretical massNumber of molelcules
Total (without water)252,2468
Polymers252,2468
Non-polymers00
Water10,142563
1
A: Enoyl-(acyl-carrier-protein) reductase (NADH)
B: Enoyl-(acyl-carrier-protein) reductase (NADH)
C: Enoyl-(acyl-carrier-protein) reductase (NADH)
D: Enoyl-(acyl-carrier-protein) reductase (NADH)


Theoretical massNumber of molelcules
Total (without water)126,1234
Polymers126,1234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-92 kcal/mol
Surface area33050 Å2
MethodPISA
2
E: Enoyl-(acyl-carrier-protein) reductase (NADH)
F: Enoyl-(acyl-carrier-protein) reductase (NADH)
G: Enoyl-(acyl-carrier-protein) reductase (NADH)
H: Enoyl-(acyl-carrier-protein) reductase (NADH)


Theoretical massNumber of molelcules
Total (without water)126,1234
Polymers126,1234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-91 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 120.100, 137.700
Angle α, β, γ (deg.)90.000, 99.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-(acyl-carrier-protein) reductase (NADH)


Mass: 31530.762 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Expressed with a N-terminal hexahis tag and 3C protease cleavage site but crystallized protein was not cleaved
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biovar Abortus 2308 / Gene: BMEI1512 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YFK8, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PACT Premier screen condition C11, 20% PEG 6000, 0.2 M CaCl2, 0.1 M HEPES NaOH pH 7.0, 47.3 mg/mL protein, crystal ID 200296c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 84019 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.157 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.3
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.6 / Num. measured obs: 16977 / Num. unique all: 5125 / Num. unique obs: 5125 / % possible all: 79.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU B: 8.008 / SU ML: 0.192 / SU R Cruickshank DPI: 0.48 / SU Rfree: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4211 5 %RANDOM
Rwork0.206 ---
obs0.209 84017 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.06 Å2 / Biso mean: 27.873 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.04 Å2
2---0.34 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15116 0 0 563 15679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210054
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.95620845
X-RAY DIFFRACTIONr_angle_other_deg0.816324482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71151982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44523.815650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.019152490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.091593
X-RAY DIFFRACTIONr_chiral_restr0.0610.22393
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023186
X-RAY DIFFRACTIONr_mcbond_it0.5431.59830
X-RAY DIFFRACTIONr_mcbond_other0.0811.54132
X-RAY DIFFRACTIONr_mcangle_it1.028215589
X-RAY DIFFRACTIONr_scbond_it1.33335550
X-RAY DIFFRACTIONr_scangle_it2.2474.55256
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 255 -
Rwork0.261 4799 -
all-5054 -
obs--79.04 %

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