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- PDB-1pox: THE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PY... -

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Basic information

Entry
Database: PDB / ID: 1pox
TitleTHE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PYRUVATE OXIDASE FROM LACTOBACILLUS PLANTARUM
ComponentsPYRUVATE OXIDASE
KeywordsOXIDOREDUCTASE(OXYGEN AS ACCEPTOR)
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 / THIAMINE DIPHOSPHATE / Pyruvate oxidase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMuller, Y.A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum.
Authors: Muller, Y.A. / Schumacher, G. / Rudolph, R. / Schulz, G.E.
#1: Journal: Science / Year: 1993
Title: Structure of the Thiamine-and Flavin-Dependent Enzyme Pyruvate Oxidase
Authors: Muller, Y.A. / Schulz, G.E.
History
DepositionNov 9, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_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.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_ref_seq_dif.details / _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: PYRUVATE OXIDASE
B: PYRUVATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,11512
Polymers128,4152
Non-polymers2,70110
Water13,313739
1
A: PYRUVATE OXIDASE
B: PYRUVATE OXIDASE
hetero molecules

A: PYRUVATE OXIDASE
B: PYRUVATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,23124
Polymers256,8304
Non-polymers5,40120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area33720 Å2
ΔGint-226 kcal/mol
Surface area70250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.600, 155.400, 167.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: THE NA+ ION IS LOCATED ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS.
2: HOH 801 - 806 ARE LOCATED ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS.
Components on special symmetry positions
IDModelComponents
11A-614-

NA

21B-614-

NA

31A-976-

HOH

41A-977-

HOH

51A-978-

HOH

61A-979-

HOH

71B-987-

HOH

81B-988-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999948, 0.008221, -0.006109), (-0.001108, -0.679808, -0.733389), (-0.010182, -0.733344, 0.679782)
Vector: -9.915, 130.53011, 56.622)
DetailsTHE TETRAMER CAN BE GENERATED FROM THE ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSFORMATION: 1 0 0 0 0 -1 0 155.36 0 0 -1 0 THE TWO SUBUNITS OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT ARE RELATED BY A LOCAL TWOFOLD AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PYRUVATE OXIDASE


Mass: 64207.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / References: UniProt: P37063, pyruvate oxidase

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Non-polymers , 6 types, 749 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


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


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme 1drop
250 mMpotasssium phosphate1drop
35 %(v/v)glycerol1drop
40.5 Mammonium sulphate1drop
51 mMThDP1drop
60.95 Mammonium sulfate1reservoir
750 mMpotassium phosphate1reservoir
810 %(v/v)glycerol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 88000 / % possible obs: 95.6 % / Num. measured all: 280000 / Rmerge(I) obs: 0.122

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→10 Å /
RfactorNum. reflection
Rwork0.162 -
obs0.162 87755
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 174 739 9961
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Num. reflection obs: 87755 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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