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- PDB-3n6q: Crystal structure of YghZ from E. coli -

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Basic information

Entry
Database: PDB / ID: 3n6q
TitleCrystal structure of YghZ from E. coli
ComponentsYghZ aldo-keto reductase
KeywordsOXIDOREDUCTASE / TIM barrel
Function / homology
Function and homology information


methylglyoxal catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / DNA damage response
Similarity search - Function
: / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-glyceraldehyde 3-phosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZubieta, C. / Totir, M. / Echols, N. / May, A. / Alber, T.
CitationJournal: Plos One / Year: 2012
Title: Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.
Authors: Totir, M. / Echols, N. / Nanao, M. / Gee, C.L. / Moskaleva, A. / Gradia, S. / Iavarone, A.T. / Berger, J.M. / May, A.P. / Zubieta, C. / Alber, T.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: YghZ aldo-keto reductase
B: YghZ aldo-keto reductase
C: YghZ aldo-keto reductase
D: YghZ aldo-keto reductase
E: YghZ aldo-keto reductase
F: YghZ aldo-keto reductase
G: YghZ aldo-keto reductase
H: YghZ aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,22717
Polymers311,0098
Non-polymers2199
Water47,5962642
1
A: YghZ aldo-keto reductase
B: YghZ aldo-keto reductase
C: YghZ aldo-keto reductase
D: YghZ aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,6269
Polymers155,5044
Non-polymers1225
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-60 kcal/mol
Surface area48060 Å2
MethodPISA
2
E: YghZ aldo-keto reductase
F: YghZ aldo-keto reductase
G: YghZ aldo-keto reductase
H: YghZ aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,6028
Polymers155,5044
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-50 kcal/mol
Surface area47850 Å2
MethodPISA
3
A: YghZ aldo-keto reductase
B: YghZ aldo-keto reductase
C: YghZ aldo-keto reductase
D: YghZ aldo-keto reductase
hetero molecules

E: YghZ aldo-keto reductase
F: YghZ aldo-keto reductase
G: YghZ aldo-keto reductase
H: YghZ aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,22717
Polymers311,0098
Non-polymers2199
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area20970 Å2
ΔGint-163 kcal/mol
Surface area89910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.700, 98.056, 98.257
Angle α, β, γ (deg.)90.27, 92.97, 106.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
YghZ aldo-keto reductase


Mass: 38876.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: DH5alpha / References: UniProt: Q46851
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2642 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M MgFormate, 0.1M MES pH 6, 7.5% PEG 20,000, 4% 1,4 butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 193K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→98 Å / Num. all: 294303 / Num. obs: 294303 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.2 / Num. unique all: 42267 / Rsym value: 0.568 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A79

2a79


Resolution: 1.8→94.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.462 / SU ML: 0.075 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 1.3 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 14824 5.1 %RANDOM
Rwork0.16875 ---
obs0.17077 277925 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.7 Å20.34 Å2
2---0.52 Å2-0.22 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→94.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19673 0 9 2642 22324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02120400
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.96227685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58552570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75324.042997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.701153518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.15215157
X-RAY DIFFRACTIONr_chiral_restr0.1370.23003
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02115681
X-RAY DIFFRACTIONr_mcbond_it1.4751.512503
X-RAY DIFFRACTIONr_mcangle_it2.359219960
X-RAY DIFFRACTIONr_scbond_it3.76337897
X-RAY DIFFRACTIONr_scangle_it5.8764.57681
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 1065 -
Rwork0.329 19950 -
obs-19950 93.25 %

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