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- PDB-7tmb: Crystal Structure of N-ethylmaleimide reductase from Klebsiella p... -

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Basic information

Entry
Database: PDB / ID: 7tmb
TitleCrystal Structure of N-ethylmaleimide reductase from Klebsiella pneumoniae
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / N-ethylmaleimide reductase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyNADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / CITRATE ANION / FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal Structure of N-ethylmaleimide reductase from Klebsiella pneumoniae
Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
C: N-ethylmaleimide reductase
D: N-ethylmaleimide reductase
E: N-ethylmaleimide reductase
F: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,21136
Polymers242,8706
Non-polymers6,34130
Water25,4911415
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3465
Polymers40,4781
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7247
Polymers40,4781
Non-polymers1,2466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.307, 223.870, 223.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
N-ethylmaleimide reductase


Mass: 40478.305 Da / Num. of mol.: 6 / Fragment: KlpnC.00093.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_29700 / Plasmid: KlpnC.00093.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GQS4

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Non-polymers , 5 types, 1445 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1415 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.6 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index H10: 20 % (w/v) PEG 3350, 0.2 M Sodium citrate tribasic dihydrate, KlpnC.00093.a.B1.PS39081 at 18.3 mg/mL, Tray: plate 12226 well H10 drop 1, Puck: PSL0405, Cryo: 80% crystallant and 20% PEG 200,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.24 Å / Num. obs: 190392 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10 / Num. measured all: 1290315 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.1-2.146.60.846144093410.8722.199.9
11.5-49.246.30.035806112710.99927.198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.20_4474refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P62

3p62


Resolution: 2.1→25.54 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 9429 4.97 %
Rwork0.1923 180468 -
obs0.1943 189897 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 30.6636 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 2.1→25.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16390 0 395 1415 18200
Biso mean--49.48 32.77 -
Num. residues----2165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.120.30593350.270559376272100
2.12-2.150.27272690.254160036272100
2.15-2.180.28573000.253659996299100
2.18-2.20.28413190.243959516270100
2.2-2.230.27773220.242759836305100
2.23-2.260.29283230.229959426265100
2.26-2.290.26942750.223260106285100
2.29-2.330.27412760.216860466322100
2.33-2.360.2443120.212159786290100
2.36-2.40.24633520.218359596311100
2.4-2.450.26373190.216859856304100
2.45-2.490.25963230.210359596282100
2.49-2.540.2773190.206159996318100
2.54-2.590.27863010.21459776278100
2.59-2.650.27672980.211660106308100
2.65-2.710.26533380.201759846322100
2.71-2.770.22662480.20360506298100
2.77-2.850.2412640.202460526316100
2.85-2.930.23753180.193460066324100
2.93-3.030.23033190.202460456364100
3.03-3.140.24943420.203459706312100
3.14-3.260.23262910.206960336324100
3.26-3.410.23863560.199460236379100
3.41-3.590.21713080.187660446352100
3.59-3.810.22293600.17160016361100
3.81-4.110.1763180.152160656383100
4.11-4.520.1863050.141660966401100
4.52-5.170.17253590.144760616420100
5.17-6.490.20463110.165361766487100
6.49-25.540.20533490.18596124647397

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