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- PDB-4keq: Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound -

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Basic information

Entry
Database: PDB / ID: 4keq
TitleCrystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound
Components4-pyridoxolactonase
KeywordsHYDROLASE / alpha-beta/beta-alpha fold / lactone
Function / homology
Function and homology information


4-pyridoxolactonase / 4-pyridoxolactonase activity / vitamin B6 catabolic process / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one / 4-pyridoxolactonase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.279 Å
AuthorsKobayashi, J. / Yoshikane, Y. / Baba, S. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of 4-pyridoxolactonase from Mesorhizobium loti.
Authors: Kobayashi, J. / Yoshikane, Y. / Yagi, T. / Baba, S. / Mizutani, K. / Takahashi, N. / Mikami, B.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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

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Assembly

Deposited unit
A: 4-pyridoxolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,64911
Polymers30,7261
Non-polymers92410
Water73941
1
A: 4-pyridoxolactonase
hetero molecules

A: 4-pyridoxolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,29822
Polymers61,4512
Non-polymers1,84720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
2
A: 4-pyridoxolactonase
hetero molecules

A: 4-pyridoxolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,29822
Polymers61,4512
Non-polymers1,84720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.426, 39.576, 84.660
Angle α, β, γ (deg.)90.00, 117.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-pyridoxolactonase


Mass: 30725.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6805 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988B9, 4-pyridoxolactonase

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5PN / 7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one / 5-Pyridoxolactone


Mass: 165.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.05M ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDetector: CCD / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.279→50 Å / Num. obs: 11493 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.71 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 30.3
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 12.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AJ0

3aj0
PDB Unreleased entry


Resolution: 2.279→36.182 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 552 4.81 %Random
Rwork0.1882 ---
obs0.1909 11484 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.59 Å2 / Biso mean: 23.3836 Å2 / Biso min: 8.06 Å2
Refinement stepCycle: LAST / Resolution: 2.279→36.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 56 41 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052269
X-RAY DIFFRACTIONf_angle_d1.0713070
X-RAY DIFFRACTIONf_chiral_restr0.076316
X-RAY DIFFRACTIONf_plane_restr0.004401
X-RAY DIFFRACTIONf_dihedral_angle_d15.951821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2786-2.50780.29221460.2042677282399
2.5078-2.87060.32331310.222727282859100
2.8706-3.61610.25161350.194127412876100
3.6161-36.18690.20071400.16692786292699

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