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- PDB-3d3f: Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3d3f
TitleCrystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis
ComponentsYvgN protein
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE
Function / homology
Function and homology information


methylglyoxal reductase (NADPH) / methylglyoxal reductase (NADPH) activity / small molecule metabolic process / organic substance metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
Aldo-keto reductase family 5G / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 5G / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Glyoxal reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZhou, Y.F. / Lei, J. / Su, X.D.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis
Authors: Lei, J. / Zhou, Y.F. / Li, L.F. / Su, X.-D.
History
DepositionMay 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: YvgN protein
B: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6404
Polymers63,1502
Non-polymers1,4912
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3202
Polymers31,5751
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3202
Polymers31,5751
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.517, 123.285, 57.226
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 YvgN protein / Putative reductase protein / YvgN


Mass: 31574.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yvgN / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32210
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 45.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.4M SODIUM NITRATE, 40% PEG3350, pH 7.5, Vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: SMART6000 / Detector: CCD / Date: Dec 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→67.4 Å / Num. all: 26027 / Num. obs: 23334 / % possible obs: 89 % / Redundancy: 14 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 5.26
Reflection shellResolution: 2.3→2.47 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 5.26 / Num. unique all: 23334 / Rsym value: 0.11 / % possible all: 89

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.384 / Cor.coef. Fo:Fc: 0.716
Highest resolutionLowest resolution
Rotation3 Å67.42 Å
Translation3 Å67.42 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUMdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B3E

3b3e
PDB Unreleased entry


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / SU B: 21.879 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.916 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30615 1065 5 %RANDOM
Rwork0.23649 ---
obs0.24007 20421 93.75 %-
all-26027 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.578 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---3.37 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 96 81 4629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224643
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9836291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2075548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33825.507227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1115846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1011520
X-RAY DIFFRACTIONr_chiral_restr0.1570.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023456
X-RAY DIFFRACTIONr_nbd_refined0.2320.22400
X-RAY DIFFRACTIONr_nbtor_refined0.310.23055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.25
X-RAY DIFFRACTIONr_mcbond_it0.7161.52840
X-RAY DIFFRACTIONr_mcangle_it1.16624407
X-RAY DIFFRACTIONr_scbond_it1.98332095
X-RAY DIFFRACTIONr_scangle_it2.9634.51884
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 38 -
Rwork0.264 1008 -
all-1046 -
obs--63.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81560.11840.02861.4120.38962.5456-0.027-0.01990.0027-0.027-0.0061-0.031-0.0635-0.05020.0332-0.13540.0084-0.0016-0.09980.0214-0.0834-17.905412.1735-21.8502
21.1006-0.2620.23492.23830.34882.81230.00550.0260.02960.0569-0.0035-0.01520.19130.0093-0.002-0.1190.00640.0046-0.09790.019-0.1099-19.110343.2027-6.6203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 2709 - 269
2X-RAY DIFFRACTION2BB10 - 2709 - 269

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