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

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Basic information

Entry
Database: PDB / ID: 2wvh
TitleStructural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE / THIAMINE DIPHOSPHATE / FLAVOPROTEIN / METAL-BINDING / ALCOHOL FERMENTATION
Function / homology
Function and homology information


pyruvate decarboxylase / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding
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
Pyruvate decarboxylase
Similarity search - Component
Biological speciesZYMOMONAS MOBILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 16, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)487,9238
Polymers487,9238
Non-polymers00
Water74,6724145
1
V: PYRUVATE DECARBOXYLASE
X: PYRUVATE DECARBOXYLASE
Y: PYRUVATE DECARBOXYLASE
Z: PYRUVATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)243,9614
Polymers243,9614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23190 Å2
ΔGint-113.9 kcal/mol
Surface area67420 Å2
MethodPISA
2
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
E: PYRUVATE DECARBOXYLASE
F: PYRUVATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)243,9614
Polymers243,9614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-111.2 kcal/mol
Surface area67590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.901, 111.175, 167.118
Angle α, β, γ (deg.)89.89, 90.87, 101.27
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 2:564 )
211CHAIN B AND (RESSEQ 2:564 )
311CHAIN E AND (RESSEQ 2:564 )
411CHAIN F AND (RESSEQ 2:564 )
511CHAIN X AND (RESSEQ 2:564 )
611CHAIN Y AND (RESSEQ 2:564 )
711CHAIN V AND (RESSEQ 2:564 )
811CHAIN Z AND (RESSEQ 2:564 )

NCS oper:
IDCodeMatrixVector
1given(-0.9997, -0.02407, -0.008737), (-0.02295, 0.6909, 0.7226), (-0.01135, 0.7225, -0.6912)1.15, -0.04896, 0.1025
2given(0.9997, 0.02339, 0.01151), (0.02335, -0.9997, 0.003806), (0.0116, -0.003536, -0.9999)-0.0192, 0.3485, 0.3398
3given(-1, 0.00067, -0.001708), (0.000767, -0.6933, -0.7207), (-0.001667, -0.7207, 0.6932)1.251, 0.4521, 0.1432
4given(0.9997, 0.02317, 0.01204), (0.007403, -0.6937, 0.7203), (0.02504, -0.7199, -0.6936)-7.38, 60.63, -57.24
5given(-0.9998, 0.000748, -0.02213), (-0.000675, -1, -0.003286), (-0.02213, -0.003271, 0.9997)7.791, 0.7031, 83.61
6given(0.9998, -0.001661, 0.01869), (0.01459, 0.6951, -0.7188), (-0.01179, 0.7189, 0.695)-6.988, -60.26, 57.47
7given(-0.9997, -0.02168, -0.01082), (-0.02175, 0.9997, 0.006596), (0.01068, 0.00683, -0.9999)8.739, 0.1087, -83.12

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4145 / 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: 2.78 Å3/Da / Density % sol: 0.55 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 7.5
Details: VAPOUR DIFFUSION. RESERVIOR CONTAINS FLUORIDE 0.2 M AND PEG3350 20% W/V., PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 798597 / % possible obs: 98.1 % / Observed criterion σ(I): 2.5 / Redundancy: 3.7 % / Biso Wilson estimate: 26.89 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 97.3

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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: 2.3→16.97 Å / SU ML: 0.83 / σ(F): 0.56 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 21281 5 %
Rwork0.171 --
obs0.172 423906 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.72 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.979 Å22.6402 Å2-3.4735 Å2
2--3.1308 Å21.1796 Å2
3----5.1098 Å2
Refinement stepCycle: LAST / Resolution: 2.3→16.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34127 0 0 4145 38272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534851
X-RAY DIFFRACTIONf_angle_d0.87247385
X-RAY DIFFRACTIONf_dihedral_angle_d16.15612315
X-RAY DIFFRACTIONf_chiral_restr0.0615345
X-RAY DIFFRACTIONf_plane_restr0.0036179
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4238X-RAY DIFFRACTIONPOSITIONAL
12B4238X-RAY DIFFRACTIONPOSITIONAL0.035
13E4248X-RAY DIFFRACTIONPOSITIONAL0.033
14F4248X-RAY DIFFRACTIONPOSITIONAL0.034
15X4248X-RAY DIFFRACTIONPOSITIONAL0.034
16Y4248X-RAY DIFFRACTIONPOSITIONAL0.029
17V4248X-RAY DIFFRACTIONPOSITIONAL0.028
18Z4248X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.24356560.220513319X-RAY DIFFRACTION95
2.3261-2.35340.26187150.223813579X-RAY DIFFRACTION95
2.3534-2.3820.24076910.222413382X-RAY DIFFRACTION95
2.382-2.41210.24826740.221813327X-RAY DIFFRACTION95
2.4121-2.44370.26146810.215113605X-RAY DIFFRACTION95
2.4437-2.47710.23487170.212713238X-RAY DIFFRACTION96
2.4771-2.51240.25176800.212713507X-RAY DIFFRACTION95
2.5124-2.54980.25526760.214513493X-RAY DIFFRACTION96
2.5498-2.58950.23087350.205713287X-RAY DIFFRACTION95
2.5895-2.63180.23057190.196713484X-RAY DIFFRACTION96
2.6318-2.6770.22817040.195613363X-RAY DIFFRACTION95
2.677-2.72550.22267430.194413579X-RAY DIFFRACTION96
2.7255-2.77770.23436640.199713345X-RAY DIFFRACTION96
2.7777-2.83410.2237150.196313457X-RAY DIFFRACTION96
2.8341-2.89540.23897290.194213337X-RAY DIFFRACTION95
2.8954-2.96240.21347470.18613389X-RAY DIFFRACTION96
2.9624-3.03610.20887360.18113333X-RAY DIFFRACTION96
3.0361-3.11770.18516990.177913466X-RAY DIFFRACTION96
3.1177-3.20890.18357800.163513403X-RAY DIFFRACTION96
3.2089-3.31170.18077000.159413295X-RAY DIFFRACTION95
3.3117-3.42910.16766910.151813429X-RAY DIFFRACTION95
3.4291-3.56520.17487880.154413450X-RAY DIFFRACTION96
3.5652-3.72580.20537430.183713309X-RAY DIFFRACTION95
3.7258-3.920.16247200.145413184X-RAY DIFFRACTION95
3.92-4.16220.16317260.140613366X-RAY DIFFRACTION95
4.1622-4.47810.13886720.12913338X-RAY DIFFRACTION95
4.4781-4.91870.14516640.125113257X-RAY DIFFRACTION94
4.9187-5.60790.1726680.152213349X-RAY DIFFRACTION95
5.6079-6.98240.17587260.149713929X-RAY DIFFRACTION99
6.9824-16.96670.14597220.136113826X-RAY DIFFRACTION98
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)
10.0453-0.0026-0.05410.1294-0.08640.2440.04-0.01440.00760.0293-0.03530.0352-0.11280.066-0.12530.0458-0.02680.00130.0154-0.02940.0687-7.726926.1347-6.3411
20.02780.0083-0.09570.1829-0.03190.12850.0272-0.09010.02090.1205-0.0464-0.0312-0.05840.1489-0.21440.072-0.061-0.03450.1445-0.01450.01698.363613.68423.3867
30.05140.0195-0.02840.24230.02310.2690.0002-0.0125-0.02320.0613-0.04570.05340.12530.0584-0.12390.07690.02090.02340.00930.00010.0632-7.2563-25.94246.6671
40.04350.0263-0.00030.10040.0080.1505-0.01220.044-0.0238-0.0088-0.0064-0.01930.06720.1071-0.0650.03350.04090.01430.1006-0.0110.05349.0851-13.1575-22.9772
50.0180.00240.03840.09150.02680.11730.0237-0.0681-0.01390.043-0.04970.00720.0598-0.1473-0.04420.0318-0.05710.02030.17270.00940.02910.6411-12.7716-60.1054
60.0078-0.02020.04160.0529-0.04830.1410.0021-0.00820.0027-0.0112-0.0334-0.01880.0575-0.0185-0.4538-0.0291-0.0129-0.0056-0.04790.0185-0.052617.5619-25.1578-89.6475
70.02020.0156-0.04880.1681-0.02970.12870.01080.07370.014-0.0788-0.0391-0.0032-0.0651-0.1343-0.08740.07270.0718-0.0240.16390.00570.0211.200114.1988-106.4557
80.0532-0.0065-0.01660.16480.00940.2970.02450.00270.00130.0154-0.0576-0.0744-0.1411-0.0672-0.08110.07680.0279-0.00920.02350.02120.061816.787326.9127-76.4494
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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