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- PDB-2vbf: The holostructure of the branched-chain keto acid decarboxylase (... -

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Basic information

Entry
Database: PDB / ID: 2vbf
TitleThe holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis
ComponentsBRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE
KeywordsLYASE / KDCA / FLAVOPROTEIN / THDP-DEPENDENT ENZYMES / THIAMINE PYROPHOSPHATE
Function / homology
Function and homology information


branched-chain-2-oxoacid decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / branched-chain amino acid biosynthetic process / 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 / Branched-chain alpha-ketoacid decarboxylase
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBerthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction
Authors: Berthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G.
History
DepositionSep 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE
B: BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7126
Polymers126,8132
Non-polymers8994
Water19,9791109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-60.1 kcal/mol
Surface area46070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.603, 108.421, 146.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B-11 - -6
2114A-11 - -6

NCS oper:
IDCodeMatrixVector
1given(0.443, -0.646, -0.622), (-0.643, -0.712, 0.282), (-0.624, 0.275, -0.731)88.80892, 182.40291, 16.90536
2given(0.432, -0.675, -0.598), (-0.689, -0.675, 0.263), (-0.581, 0.299, -0.757)90.70049, 181.44542, 14.40747

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Components

#1: Protein BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE / BRANCHED-CHAIN KETO ACID DECARBOXYLASE


Mass: 63406.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAIN A AND B CONTAIN THE COMPLETE ENZYME SEQUENCE AND SHORT N-TERMINAL TAGS WITH LINKERS, WHICH ARE BOUND IN ADJACENT DIMERS IN THE CRYSTAL.
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6QBS4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CONTAINS A 23 AMINO ACID N-TERMINAL EXTENSION, MGSSHHHHHHSSGLVPRGSHMAS

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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: 1.9 Å3/Da / Density % sol: 34.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→56.17 Å / Num. obs: 127559 / % possible obs: 92.4 % / Observed criterion σ(I): 6 / Redundancy: 3.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 63.8

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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 1OVM

1ovm


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.674 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES 182-187 HAVE NOT BEEN MODELED DUE TO LACK OF ELECTRON DENSITY THE FLEXIBLE REGION B 538-547 WAS MODELED AT OCCUPANCY 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6436 5 %RANDOM
Rwork0.163 ---
obs0.165 121047 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8564 0 54 1109 9727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228865
X-RAY DIFFRACTIONr_bond_other_d0.0010.025912
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9712034
X-RAY DIFFRACTIONr_angle_other_deg0.891314544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55751121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85125.414399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.333151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4691530
X-RAY DIFFRACTIONr_chiral_restr0.070.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
X-RAY DIFFRACTIONr_nbd_refined0.2040.21898
X-RAY DIFFRACTIONr_nbd_other0.1820.26411
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24410
X-RAY DIFFRACTIONr_nbtor_other0.0820.24307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2908
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.47237151
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6648857
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.85343956
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.53253159
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

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 55 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.130.5
medium thermal0.742
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 300
Rwork0.249 5619

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