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- PDB-2wva: Structural insights into the pre-reaction state of pyruvate decar... -

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Basic information

Entry
Database: PDB / ID: 2wva
TitleStructural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE / THIAMIN DIPHOSPHATE / FLAVOPROTEIN / METAL-BINDING / ALCOHOL FERMENTATION
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
PYRUVIC ACID / Chem-TPU / Pyruvate decarboxylase
Similarity search - Component
Biological speciesZYMOMONAS MOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPei, X.Y. / Erixon, K. / Luisi, B.F. / Leeper, F.J.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase from Zymomonas Mobilis
Authors: Pei, X.Y. / Erixon, K. / Luisi, B.F. / Leeper, F.J.
History
DepositionOct 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
V: PYRUVATE DECARBOXYLASE
X: PYRUVATE DECARBOXYLASE
Y: PYRUVATE DECARBOXYLASE
Z: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,64727
Polymers487,9238
Non-polymers3,72519
Water47,9742663
1
V: PYRUVATE DECARBOXYLASE
X: PYRUVATE DECARBOXYLASE
Y: PYRUVATE DECARBOXYLASE
Z: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,86814
Polymers243,9614
Non-polymers1,90610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28420 Å2
ΔGint-167.1 kcal/mol
Surface area63630 Å2
MethodPISA
2
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
E: PYRUVATE DECARBOXYLASE
F: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,78013
Polymers243,9614
Non-polymers1,8189
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28140 Å2
ΔGint-173.5 kcal/mol
Surface area63760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.619, 111.585, 167.432
Angle α, β, γ (deg.)89.82, 90.11, 78.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:565 )
211CHAIN B AND (RESSEQ 2:565 )
311CHAIN E AND (RESSEQ 2:565 )
411CHAIN F AND (RESSEQ 2:565 )
511CHAIN X AND (RESSEQ 2:565 )
611CHAIN Y AND (RESSEQ 2:565 )
711CHAIN V AND (RESSEQ 2:565 )
811CHAIN Z AND (RESSEQ 2:565 )

NCS oper:
IDCodeMatrixVector
1given(-0.9998, 0.01807, -0.008517), (0.01866, 0.6925, -0.7212), (-0.007135, -0.7212, -0.6927)-0.2284, -0.00322, -0.02674
2given(-1, 0.001253, -0.002173), (-0.001261, -1, 0.003988), (-0.002168, 0.003991, 1)-7.003, 0.8857, 83.73
3given(0.9996, -0.02682, -0.01051), (-0.02687, -0.9996, -0.004498), (-0.01038, 0.004779, -0.9999)-0.01826, -0.01709, 0.0526
4given(0.9998, -0.01939, -0.007185), (-0.01865, -0.6954, -0.7184), (0.008936, 0.7184, -0.6956)5.943, -59.95, -58.58
5given(-0.9998, 0.007992, 0.02018), (0.008962, -0.6947, 0.7192), (0.01977, 0.7192, 0.6945)-0.2668, -0.01691, -0.03341
6given(0.9997, -0.007679, 0.02118), (-0.009836, 0.6969, 0.7171), (-0.02027, -0.7171, 0.6967)8.382, 59.51, 58.59
7given(-0.9996, 0.0258, -0.01184), (0.02589, 0.9996, -0.007765), (0.01163, -0.008069, -0.9999)-7.812, -1.029, -83.54

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Components

#1: Protein
PYRUVATE DECARBOXYLASE / / PDC


Mass: 60990.328 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZYMOMONAS MOBILIS (bacteria) / Plasmid: PPL450 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / References: UniProt: P06672, pyruvate decarboxylase
#2: Chemical
ChemComp-TPU / 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYL TRIHYDROGEN DIPHOSPHATE


Mass: 408.244 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N6O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2663 / 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: 2.7 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 7.5
Details: CO-CRYSTALLISATION USING VAPOUR DIFFUSION METHODS. A RESERVIOR CONTAINING POTASSIUM CHLORIDE 0.2 M, PEG3350 17% W/V AND XYLITOL 3 OR 1.5% W/V, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.951
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 214702 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZPD

1zpd


Resolution: 2.2→34.65 Å / SU ML: 0.44 / σ(F): 0.59 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 21216 5.1 %
Rwork0.194 --
obs0.195 419578 82.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.39 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.5853 Å2-10.3775 Å2-1.5632 Å2
2--22.262 Å21.2742 Å2
3----21.2084 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34136 0 234 2663 37033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935128
X-RAY DIFFRACTIONf_angle_d1.02147790
X-RAY DIFFRACTIONf_dihedral_angle_d17.56212489
X-RAY DIFFRACTIONf_chiral_restr0.0715327
X-RAY DIFFRACTIONf_plane_restr0.0056221
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4249X-RAY DIFFRACTIONPOSITIONAL
12B4249X-RAY DIFFRACTIONPOSITIONAL0.1
13E4255X-RAY DIFFRACTIONPOSITIONAL0.148
14F4255X-RAY DIFFRACTIONPOSITIONAL0.108
15X4249X-RAY DIFFRACTIONPOSITIONAL0.089
16Y4255X-RAY DIFFRACTIONPOSITIONAL0.102
17V4255X-RAY DIFFRACTIONPOSITIONAL0.096
18Z4249X-RAY DIFFRACTIONPOSITIONAL0.115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.46963150.45865842X-RAY DIFFRACTION36
2.225-2.25120.46123460.43266337X-RAY DIFFRACTION40
2.2512-2.27860.42363580.41026902X-RAY DIFFRACTION42
2.2786-2.30750.36943790.38887555X-RAY DIFFRACTION47
2.3075-2.33780.36374100.36718204X-RAY DIFFRACTION51
2.3378-2.36980.36774970.35898956X-RAY DIFFRACTION56
2.3698-2.40370.3864870.34349730X-RAY DIFFRACTION61
2.4037-2.43960.34915110.326810821X-RAY DIFFRACTION66
2.4396-2.47770.33476370.318911987X-RAY DIFFRACTION75
2.4777-2.51830.30518030.291814548X-RAY DIFFRACTION90
2.5183-2.56170.3018130.284315276X-RAY DIFFRACTION96
2.5617-2.60830.28498130.269715636X-RAY DIFFRACTION96
2.6083-2.65840.29698350.263115316X-RAY DIFFRACTION96
2.6584-2.71260.26388400.251615642X-RAY DIFFRACTION96
2.7126-2.77160.27038180.248515210X-RAY DIFFRACTION96
2.7716-2.8360.2748640.237615570X-RAY DIFFRACTION96
2.836-2.90690.2478860.229115276X-RAY DIFFRACTION96
2.9069-2.98550.22878080.217115510X-RAY DIFFRACTION96
2.9855-3.07330.22078740.209515588X-RAY DIFFRACTION96
3.0733-3.17240.24617930.199815392X-RAY DIFFRACTION96
3.1724-3.28570.20448250.193115414X-RAY DIFFRACTION96
3.2857-3.41720.18918710.181615398X-RAY DIFFRACTION96
3.4172-3.57250.21038240.17715441X-RAY DIFFRACTION96
3.5725-3.76070.17217520.158715458X-RAY DIFFRACTION95
3.7607-3.9960.17518410.153215415X-RAY DIFFRACTION96
3.996-4.3040.15768000.133515406X-RAY DIFFRACTION95
4.304-4.73620.14327990.125815227X-RAY DIFFRACTION95
4.7362-5.41920.16188520.142715200X-RAY DIFFRACTION94
5.4192-6.81910.1587500.144914659X-RAY DIFFRACTION91
6.8191-34.65850.14738150.139515446X-RAY DIFFRACTION96
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)
10.24450.12080.11650.07820.05820.9122-0.0026-0.0141-0.0871-0.00030.0109-0.0465-0.1761-0.1151-0.00040.260.0354-0.00290.2593-0.00060.2668.304425.73776.2457
20.0440.0369-0.05330.26180.21640.5558-0.01770.06740.0077-0.1376-0.0192-0.0074-0.1215-0.36830.03450.29730.0189-0.03330.56690.03820.2173-8.132313.4691-23.0277
30.27380.0372-0.13660.1377-0.00780.7605-0.01560.00490.0191-0.0254-0.0016-0.06230.2501-0.12490.01220.3536-0.10290.02740.3035-0.0250.29917.545-25.9618-6.3847
40.0897-0.2451-0.03960.35830.13090.5575-0.0239-0.04480.03510.07930.0281-0.04490.1238-0.3249-0.0140.2493-0.10480.0140.53430.03280.2201-8.2355-13.322423.0882
50.23250.063-0.17860.119-0.07620.9866-0.0059-0.04080.0401-0.02210.01010.06170.20130.1133-0.00060.26760.0365-0.00190.25370.0140.2729-15.1306-25.181-77.3711
60.07480.00690.0110.2953-0.23010.521-0.02260.0610.0019-0.1457-0.01960.00960.12290.38440.03660.29530.0270.03690.5476-0.02460.21441.3676-13.0716-106.6959
70.26290.13120.07610.14090.0920.7783-0.0264-0.00720.0175-0.02950.0140.0914-0.27940.11990.01140.3623-0.0966-0.010.28270.03860.3068-14.356226.4729-90.1694
80.0954-0.2340.09020.347-0.15090.5832-0.0139-0.0596-0.03190.06170.01830.0417-0.13770.3288-0.01270.2527-0.1055-0.0080.5057-0.02150.22811.311214.0268-60.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN E
4X-RAY DIFFRACTION4CHAIN F
5X-RAY DIFFRACTION5CHAIN X
6X-RAY DIFFRACTION6CHAIN Y
7X-RAY DIFFRACTION7CHAIN V
8X-RAY DIFFRACTION8CHAIN Z

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