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- PDB-2ez4: Pyruvate oxidase variant F479W -

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Basic information

Entry
Database: PDB / ID: 2ez4
TitlePyruvate oxidase variant F479W
ComponentsPyruvate oxidase
KeywordsOXIDOREDUCTASE / TPP enzyme
Function / homology
Function and homology information


pyruvate oxidase / pyruvate oxidase activity / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
Pyruvate oxidase / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain ...Pyruvate oxidase / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / THIAMINE DIPHOSPHATE / Pyruvate oxidase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsWille, G. / Meyer, D. / Steinmetz, A. / Hinze, E. / Golbik, R. / Tittmann, K.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
Authors: Wille, G. / Meyer, D. / Steinmetz, A. / Hinze, E. / Golbik, R. / Tittmann, K.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Author states that residue 561 is indeed a MET. The THR from the SWS database is an error ...SEQUENCE Author states that residue 561 is indeed a MET. The THR from the SWS database is an error in the database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate oxidase
B: Pyruvate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,19812
Polymers132,4922
Non-polymers2,70610
Water17,384965
1
A: Pyruvate oxidase
B: Pyruvate oxidase
hetero molecules

A: Pyruvate oxidase
B: Pyruvate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,39624
Polymers264,9834
Non-polymers5,41320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area33370 Å2
ΔGint-264 kcal/mol
Surface area69070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.346, 154.180, 165.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1614-

NA

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x, -y+1, -z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyruvate oxidase / Pyruvic oxidase / POX


Mass: 66245.836 Da / Num. of mol.: 2 / Mutation: F479W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: pox5 / Plasmid: pBP200 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P37063, pyruvate oxidase

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Non-polymers , 6 types, 975 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 965 / 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: 2.9 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.03→99 Å / Num. all: 92857 / Num. obs: 92824 / % possible obs: 29.59 % / Observed criterion σ(F): 3.7 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 17.28 Å2 / Rmerge(I) obs: 0.107 / Χ2: 0.948 / Net I/σ(I): 10.18
Reflection shellResolution: 2.03→2.06 Å / % possible obs: 93.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.83 / Num. measured obs: 3608 / Χ2: 0.76 / % possible all: 92.95

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1POW

1pow


Resolution: 2.03→29.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.164 / WRfactor Rwork: 0.136 / SU B: 2.958 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 3.7 / ESU R: 0.146 / ESU R Free: 0.129 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 1884 2.03 %RANDOM
Rwork0.1556 ---
obs0.156 92823 94.539 %-
all-92823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.631 Å20 Å20 Å2
2---0.61 Å20 Å2
3----1.021 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 0 172 965 10183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229418
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.97412856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05451168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03825.138436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.225151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7771546
X-RAY DIFFRACTIONr_chiral_restr0.090.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027236
X-RAY DIFFRACTIONr_nbd_refined0.1980.24721
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2915
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.2253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.291
X-RAY DIFFRACTIONr_mcbond_it0.5541.55836
X-RAY DIFFRACTIONr_mcangle_it1.05629376
X-RAY DIFFRACTIONr_scbond_it1.99733743
X-RAY DIFFRACTIONr_scangle_it3.3484.53480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.03-2.0780.2091430.18665560.187720792.951
2.078-2.1350.2471270.17665820.177699895.87
2.135-2.1970.1991500.17364540.174684696.465
2.197-2.2640.1691130.16762270.167662795.669
2.264-2.3380.2341280.16360570.164644495.981
2.338-2.420.2031210.15958220.16620695.762
2.42-2.5120.1941070.16656370.167600695.638
2.512-2.6140.2151160.16253940.163579195.148
2.614-2.730.174940.16351880.163554895.205
2.73-2.8630.1711060.1649720.161535894.774
2.863-3.0180.177910.15846990.158504594.945
3.018-3.2010.1931040.15144180.152479494.326
3.201-3.4220.192850.14841640.149451994.025
3.422-3.6950.152850.13338910.133423593.884
3.695-4.0480.152600.12835770.129390393.185
4.048-4.5240.157760.12931910.13351892.865
4.524-5.2220.204620.14328230.145313392.084
5.222-6.3910.218490.18123950.181268191.16
6.391-9.0170.142420.16718570.166209490.688
9.017-94.0720.157250.15810350.158123286.039

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