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- PDB-2vbi: Holostructure of pyruvate decarboxylase from Acetobacter pasteurianus -

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Basic information

Entry
Database: PDB / ID: 2vbi
TitleHolostructure of pyruvate decarboxylase from Acetobacter pasteurianus
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE / THIAMINE PYROPHOSPHATE / PYRUVATE DECARBOXYLASE / PYRUVATE / FLAVOPROTEIN / THDP-DEPENDENT ENZYME
Function / homology
Function and homology information


pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / 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 (TPP)-dependent enzyme / : / 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
THIAMINE DIPHOSPHATE / pyruvate decarboxylase
Similarity search - Component
Biological speciesACETOBACTER PASTEURIANUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGocke, D. / Berthold, C.L. / Schneider, G. / Pohl, M.
History
DepositionSep 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
E: PYRUVATE DECARBOXYLASE
F: PYRUVATE DECARBOXYLASE
G: PYRUVATE DECARBOXYLASE
H: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,14424
Polymers489,5478
Non-polymers3,59716
Water1,65792
1
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,57212
Polymers244,7734
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27000 Å2
ΔGint-117 kcal/mol
Surface area80470 Å2
MethodPQS
2
E: PYRUVATE DECARBOXYLASE
F: PYRUVATE DECARBOXYLASE
G: PYRUVATE DECARBOXYLASE
H: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,57212
Polymers244,7734
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28570 Å2
ΔGint-123.5 kcal/mol
Surface area80670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)179.619, 162.434, 169.331
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52F
62G
72H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 201
2111B2 - 201
3111C2 - 201
4111D2 - 201
5111E2 - 201
6111F2 - 201
7111G2 - 201
8111H2 - 201
1211A211 - 558
2211B211 - 558
3211C211 - 558
4211D211 - 558
5211E211 - 558
6211F211 - 558
7211G211 - 558
8211H211 - 558
1121A2 - 558
2121B2 - 558
3121C2 - 558
4121D2 - 558
5121F2 - 558
6121G2 - 558
7121H2 - 558

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.8, 0.459, 0.386), (-0.591, 0.494, 0.638), (0.102, -0.739, 0.666)
Vector: 65.77002, -26.2087, 36.9152)

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Components

#1: Protein
PYRUVATE DECARBOXYLASE


Mass: 61193.320 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACETOBACTER PASTEURIANUS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM-NO 2347).
Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8L388, pyruvate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICTS IN THE SEQUENCE ARE KNOWN AND ARE DISCUSSED IN THE AUTHOR'S PUBLICATION. THERE ARE ...THE CONFLICTS IN THE SEQUENCE ARE KNOWN AND ARE DISCUSSED IN THE AUTHOR'S PUBLICATION. THERE ARE NINE DIFFERENT RESIDUES AND ONE MISSING RESIDUE OF THE DATABASE ENTRY OF RAJ ET AL. (NCBI ENTRY, ACCESSION NUMBER AAM21208) COMPARED TO THIS PROTEIN SEQUENCE.

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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: 51.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M)
RadiationMonochromator: BENT SILICON CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.75→39.44 Å / Num. obs: 119238 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZPD

1zpd


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU B: 31.82 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 5995 5 %RANDOM
Rwork0.224 ---
obs0.225 113173 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å2-1.56 Å2
2---3.05 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33496 0 216 92 33804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02234456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.95846944
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30254440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26624.2541448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64155472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.29715200
X-RAY DIFFRACTIONr_chiral_restr0.090.25360
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0226144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.215867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.223504
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.21005
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5050.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.131.522515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.204235304
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.404313505
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.634.511632
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4130tight positional0.010.05
12B4130tight positional0.020.05
13C4130tight positional0.020.05
14D4130tight positional0.020.05
15E4130tight positional0.030.05
16F4130tight positional0.020.05
17G4130tight positional0.010.05
18H4130tight positional0.020.05
21A4194tight positional0.010.05
22B4194tight positional0.020.05
23C4194tight positional0.020.05
24D4194tight positional0.020.05
25F4194tight positional0.020.05
26G4194tight positional0.010.05
27H4194tight positional0.020.05
11A4130tight thermal0.020.5
12B4130tight thermal0.020.5
13C4130tight thermal0.020.5
14D4130tight thermal0.030.5
15E4130tight thermal0.040.5
16F4130tight thermal0.020.5
17G4130tight thermal0.020.5
18H4130tight thermal0.020.5
21A4194tight thermal0.020.5
22B4194tight thermal0.020.5
23C4194tight thermal0.020.5
24D4194tight thermal0.030.5
25F4194tight thermal0.020.5
26G4194tight thermal0.020.5
27H4194tight thermal0.020.5
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 470
Rwork0.361 8380
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6571-0.25560.29571.86350.0981.3252-0.0667-0.1157-0.30470.28540.15450.95040.3756-0.2595-0.0878-0.1416-0.09550.1883-0.00280.12610.4588-57.0641-16.6443-12.7374
21.0118-0.07840.24591.87120.20991.0121-0.2314-0.36320.0280.84330.2180.18560.1420.00870.01350.22990.16390.06040.05160.0507-0.1856-31.0209-6.20279.6152
30.9413-0.57420.19271.8305-0.13650.7994-0.00530.06760.0496-0.09440.0078-0.37460.11240.2665-0.0025-0.2699-0.0092-0.0163-0.05640.0015-0.1174-10.49673.2376-29.2767
41.0299-0.32770.14781.7639-0.03890.6932-0.04050.0270.1126-0.20490.01450.3796-0.0101-0.06370.026-0.2553-0.0559-0.0937-0.12880.0455-0.1198-42.119118.5974-36.2003
50.40260.14630.08580.7748-0.16861.5655-0.00170.0317-0.1075-0.34030.0334-0.10640.0479-0.0167-0.0317-0.0498-0.1038-0.0069-0.14320.0179-0.1595-109.0078-14.9795-74.4188
60.44960.21550.18911.23030.15561.04840.0598-0.1357-0.09410.1223-0.0079-0.3458-0.01240.0548-0.0518-0.239-0.0771-0.0568-0.06640.0572-0.0207-92.0878-14.2967-42.8133
71.12290.013-0.00231.06740.16610.7979-0.01090.01950.092-0.24820.1076-0.4059-0.34070.2298-0.09670.073-0.2010.0815-0.053-0.0633-0.0046-85.124928.3648-54.7703
80.83940.18160.03871.20650.07790.81820.003-0.07640.0771-0.14090.0170.1691-0.347-0.2039-0.020.12850.0281-0.0346-0.08620.0393-0.1735-120.242926.5396-61.8361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 555
2X-RAY DIFFRACTION2B2 - 555
3X-RAY DIFFRACTION3C2 - 555
4X-RAY DIFFRACTION4D2 - 555
5X-RAY DIFFRACTION5E2 - 555
6X-RAY DIFFRACTION6F2 - 555
7X-RAY DIFFRACTION7G2 - 555
8X-RAY DIFFRACTION8H2 - 555

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