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- PDB-1zpd: PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS -

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Basic information

Entry
Database: PDB / ID: 1zpd
TitlePYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS
ComponentsPYRUVATE DECARBOXYLASE
KeywordsALCOHOL FERMENTATION / THIAMIN DIPHOSPHATE / DECARBOXYLASE
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 / : / 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 (TPP)-dependent 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
CITRIC ACID / Chem-DPX / Pyruvate decarboxylase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLu, G. / Dobritzsch, D. / Schneider, G.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases.
Authors: Dobritzsch, D. / Konig, S. / Schneider, G. / Lu, G.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: PYRUVATE DECARBOXYLASE
F: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,41616
Polymers243,8294
Non-polymers2,58712
Water46,2812569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30290 Å2
ΔGint-178 kcal/mol
Surface area63940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.868, 92.168, 98.256
Angle α, β, γ (deg.)102.86, 94.59, 112.69
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999996, -0.001489, -0.00241), (-0.000644, -0.709027, 0.705181), (-0.002759, 0.70518, 0.709023)0.53468, 0.13641, -0.1395
2given(0.999999, 0.000977, 0.000977), (0.000977, -1, 5.5E-5), (0.000977, -5.4E-5, -1)0.34429, -0.00492, -0.63301
3given(-0.999999, 0.001465), (-0.001031, 0.710659, -0.703536), (-0.001041, -0.703537, -0.710658)0.55823, -0.27361, -0.55083

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Components

#1: Protein
PYRUVATE DECARBOXYLASE


Mass: 60957.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Culture collection (production host): ATCC 29191 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009/PREP4 / References: UniProt: P06672, pyruvate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DPX / MONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO} ESTER


Mass: 430.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N4O8P2S
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2569 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
21 mMdithiothreitol1drop
3100 mMMes-NaOH1reservoir
424 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→22.8 Å / Num. obs: 157263 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 1.91 % / Biso Wilson estimate: 10.41 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.1
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.6 / % possible all: 62.5
Reflection
*PLUS
% possible obs: 88.2 % / Num. measured all: 306481
Reflection shell
*PLUS
% possible obs: 51.7 % / Num. unique obs: 13826 / Num. measured obs: 25442

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPD

1ypd
PDB Unreleased entry


Resolution: 1.86→15 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: NCS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND MOST WATER MOLECULES WITH CHAIN ID W, U, V, AND X, WHICH SATISFY ALL THE NCS OPERATIONS. WATER MOLECULES WITH CHAIN ID Y SATISFY 3 OF 4 NCS ...Details: NCS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND MOST WATER MOLECULES WITH CHAIN ID W, U, V, AND X, WHICH SATISFY ALL THE NCS OPERATIONS. WATER MOLECULES WITH CHAIN ID Y SATISFY 3 OF 4 NCS OPERATIONS WHILE WATERS WITH CHAIN ID Z SATISFY 2 OF 4 NCS'S. WATERS WITH CHAIN ID S DOES NOT FOLLOW ANY NCS OPERATIONS. ESD FROM SIGMAA (A) : 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.197 6858 4.3 %RANDOM
Rwork0.162 ---
obs-150215 87 %-
Displacement parametersBiso mean: 14.87 Å2
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.86→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17902 0 156 2569 20627
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.020.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 157061 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

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