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- PDB-1mcz: BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1mcz
TitleBENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE
ComponentsBENZOYLFORMATE DECARBOXYLASE
KeywordsLYASE / DECARBOXYLASE / THIAMIN DIPHOSPHATE / R-MANDELATE
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / 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 ...Thiamine pyrophosphate enzyme / 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
(R)-MANDELIC ACID / THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPolovnikova, E.S. / Bera, A.K. / Hasson, M.S.
Citation
Journal: Biochemistry / Year: 2003
Title: Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase
Authors: POLOVNIKOVA, E.S. / McLeish, M.J. / Sergienko, E.A. / Burgner, J.T. / Anderson, N.L. / BERA, A.K. / Jordan, F. / Kenyon, G.L. / HASSON, M.S.
#1: Journal: Biochemistry / Year: 1998
Title: The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes
Authors: Hasson, M.S. / Muscate, A. / McLeish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_seq_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_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN MG 529 (MAGNESIUM 2+) HAVE LOW B-FACTORS, SUGGESTING THAT THEY MAY ACTUALLY BE CALCIUM ...HETEROGEN MG 529 (MAGNESIUM 2+) HAVE LOW B-FACTORS, SUGGESTING THAT THEY MAY ACTUALLY BE CALCIUM IONS, AS IN STRUCTURE 1BFD.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BENZOYLFORMATE DECARBOXYLASE
B: BENZOYLFORMATE DECARBOXYLASE
C: BENZOYLFORMATE DECARBOXYLASE
D: BENZOYLFORMATE DECARBOXYLASE
E: BENZOYLFORMATE DECARBOXYLASE
F: BENZOYLFORMATE DECARBOXYLASE
G: BENZOYLFORMATE DECARBOXYLASE
H: BENZOYLFORMATE DECARBOXYLASE
I: BENZOYLFORMATE DECARBOXYLASE
J: BENZOYLFORMATE DECARBOXYLASE
K: BENZOYLFORMATE DECARBOXYLASE
L: BENZOYLFORMATE DECARBOXYLASE
M: BENZOYLFORMATE DECARBOXYLASE
N: BENZOYLFORMATE DECARBOXYLASE
O: BENZOYLFORMATE DECARBOXYLASE
P: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)912,26772
Polymers902,44416
Non-polymers9,82356
Water29,8331656
1
A: BENZOYLFORMATE DECARBOXYLASE
B: BENZOYLFORMATE DECARBOXYLASE
C: BENZOYLFORMATE DECARBOXYLASE
D: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,06718
Polymers225,6114
Non-polymers2,45614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28300 Å2
ΔGint-153 kcal/mol
Surface area58020 Å2
MethodPISA
2
E: BENZOYLFORMATE DECARBOXYLASE
F: BENZOYLFORMATE DECARBOXYLASE
G: BENZOYLFORMATE DECARBOXYLASE
H: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,06718
Polymers225,6114
Non-polymers2,45614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28310 Å2
ΔGint-153 kcal/mol
Surface area58070 Å2
MethodPISA
3
I: BENZOYLFORMATE DECARBOXYLASE
J: BENZOYLFORMATE DECARBOXYLASE
K: BENZOYLFORMATE DECARBOXYLASE
L: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,06718
Polymers225,6114
Non-polymers2,45614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28250 Å2
ΔGint-152 kcal/mol
Surface area58130 Å2
MethodPISA
4
M: BENZOYLFORMATE DECARBOXYLASE
N: BENZOYLFORMATE DECARBOXYLASE
O: BENZOYLFORMATE DECARBOXYLASE
P: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,06718
Polymers225,6114
Non-polymers2,45614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28230 Å2
ΔGint-151 kcal/mol
Surface area58290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.800, 209.600, 163.400
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BENZOYLFORMATE DECARBOXYLASE / BFD / BFDC


Mass: 56402.746 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: MDLC / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical
ChemComp-RMN / (R)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1656 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R- ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 20-22% PEG MME 2000, 100 mM Na citrate, pH 5.2-5.6, 0.15-0.2 M (NH4)2SO4 and 10 mM R-mandelate. DROPS CONTAINED EQUAL VOLUMES (2-4 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [20-50 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 15 MM NAHEPES (PH 7.0)]., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-50 mg/mlprotein1drop
215 mMHEPES1droppH7.0
30.2 mMThDP1drop
40.1 mM1dropMgCl2
520-22 %PEG2000MME1reservoir
6100 mMsodium citrate1reservoirpH5.2-5.6
70.15-0.2 Mammonium sulfate1reservoir
810 mM(R)-mandelate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: CuKa / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 561773 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 76.2
Reflection
*PLUS
Num. obs: 206940 / % possible obs: 94 % / Num. measured all: 561773
Reflection shell
*PLUS
% possible obs: 76 % / Rmerge(I) obs: 0.187

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFD

1bfd


Resolution: 2.8→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: NCS restraints were used on all 16 monomers from residues 2-460 and 472-525. From 461-471, NCS restraints were also applied to two groups: (1) monomers A, D, F, G, H, K and N and (2) ...Details: NCS restraints were used on all 16 monomers from residues 2-460 and 472-525. From 461-471, NCS restraints were also applied to two groups: (1) monomers A, D, F, G, H, K and N and (2) monomers B, C, E, H, I, L, M, O and P. The side chains of two residues, Phe 464 and Trp 463, are in different conformations in the two groups. In 7 out of 8 cases, the two monomers that compose two active sites in the tetramer have opposite conformations from each other.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 20500 -RANDOM
Rwork0.2 ---
all-220501 --
obs-206413 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62928 0 624 1656 65208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006892
X-RAY DIFFRACTIONc_angle_deg1.36814
LS refinement shellResolution: 2.8→2.82 Å
RfactorNum. reflection
Rfree0.3271 267
Rwork0.2953 -
obs-2657
Refinement
*PLUS
Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37

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