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- PDB-3gka: Crystal structure of N-ethylmaleimidine reductase from Burkholder... -

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Basic information

Entry
Database: PDB / ID: 3gka
TitleCrystal structure of N-ethylmaleimidine reductase from Burkholderia pseudomallei
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / deCODE biostructures / SSGCID / NIAID / targetDB BupsA00093a / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases / FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of N-ethylmaleimidine reductase from Burkholderia pseudomallei
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1274
Polymers77,2152
Non-polymers9132
Water7,152397
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0642
Polymers38,6071
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0642
Polymers38,6071
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.350, 77.890, 168.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-ethylmaleimide reductase


Mass: 38607.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BPSS0877 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63LY5, UniProt: Q3JFM9*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ sparse matrix screen condition H3, 25% PEG3350, 0.1M BisTris pH 5.5, 12.2 mg/mL BupsA00093aB1, crystal ID 200758h3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29741 / % possible obs: 99.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.82
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.97 / Num. unique all: 2179 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.55 Å
Translation3 Å19.55 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R14

2r14


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 6.147 / SU ML: 0.153 / SU R Cruickshank DPI: 0.433 / SU Rfree: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1506 5.1 %RANDOM
Rwork0.176 ---
obs0.18 29688 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.98 Å2 / Biso mean: 14.258 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.93 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 62 397 5735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225474
X-RAY DIFFRACTIONr_bond_other_d0.0010.023630
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9637485
X-RAY DIFFRACTIONr_angle_other_deg0.85338749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89522.61249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4671554
X-RAY DIFFRACTIONr_chiral_restr0.0620.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021187
X-RAY DIFFRACTIONr_mcbond_it0.3821.53491
X-RAY DIFFRACTIONr_mcbond_other0.0631.51428
X-RAY DIFFRACTIONr_mcangle_it0.7425545
X-RAY DIFFRACTIONr_scbond_it1.20731983
X-RAY DIFFRACTIONr_scangle_it2.074.51940
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 104 -
Rwork0.209 2071 -
all-2175 -
obs--99.68 %

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