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- PDB-2bp7: New crystal form of the Pseudomonas putida branched-chain dehydro... -

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Basic information

Entry
Database: PDB / ID: 2bp7
TitleNew crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)
Components
  • 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
  • 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / THDP COFACTOR
Function / homology
Function and homology information


3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain amino acid catabolic process / response to nutrient
Similarity search - Function
2-oxoisovalerate dehydrogenase, E1 alpha subunit, N-terminal domain / 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...2-oxoisovalerate dehydrogenase, E1 alpha subunit, N-terminal domain / 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal / : / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-oxoisovalerate dehydrogenase subunit alpha / 2-oxoisovalerate dehydrogenase subunit beta
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFrank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
CitationJournal: Structure / Year: 2005
Title: The Molecular Origins of Specificity in the Assembly of a Multienzyme Complex.
Authors: Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F.
History
DepositionApr 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2005Provider: 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 / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
C: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
D: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
E: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
F: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
G: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
H: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)329,9658
Polymers329,9658
Non-polymers00
Water2,486138
1
A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
C: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
D: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)164,9824
Polymers164,9824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
F: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
G: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
H: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)164,9824
Polymers164,9824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)156.866, 156.866, 619.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUAA2 - 4082 - 408
21ASNASNLEULEUCC2 - 4082 - 408
31ASNASNLEULEUEE2 - 4082 - 408
41ASNASNLEULEUGG2 - 4082 - 408
12THRTHRVALVALBB3 - 3393 - 339
22THRTHRVALVALDD3 - 3393 - 339
32THRTHRVALVALFF3 - 3393 - 339
42THRTHRVALVALHH3 - 3393 - 339

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.930318, -0.311956, 0.192853), (0.363083, 0.709174, -0.604353), (0.051766, 0.632262, 0.773023)
Vector: 44.7829, 153.35779, 33.65064)

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Components

#1: Protein
2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT / BRANCHED-CHAIN DEHYDROGENASE E1 / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA ...BRANCHED-CHAIN DEHYDROGENASE E1 / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN / BCKDH E1-ALPHA


Mass: 45318.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P09060, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Protein
2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT / BRANCHED-CHAIN DEHYDROGENASE E1 / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA ...BRANCHED-CHAIN DEHYDROGENASE E1 / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN / BCKDH E1-BETA


Mass: 37172.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P09061, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growpH: 5.6
Details: PROTEIN SAMPLE (1-5 PHOSPHATE PH6.3, 10MM DTT, 4MM MGCL2, 2MM ALPHA-CHLOROISOCAPROATE, 1MM THIAMINE DIPHOSPHATE., pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Mar 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 101157 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 33

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QS0

1qs0


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.858 / SU B: 14.934 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS PSEUODOMONAS PUTIDA BRANCHED-CHAIN DEHYDROGENASE E1 STRUCTURE IS A PACKING MODEL OF A NEW CRYSTAL FORM. THE MODEL WAS OBTAINED BY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS PSEUODOMONAS PUTIDA BRANCHED-CHAIN DEHYDROGENASE E1 STRUCTURE IS A PACKING MODEL OF A NEW CRYSTAL FORM. THE MODEL WAS OBTAINED BY MOLECULAR REPLACEMENT USING THE COORDINATES OF 1QS0, FOLLOWED BY RIGID BODY AND RESTRAINED REFINEMENT. NO MANUAL FITTING OF THE MODEL WAS PERFORMED.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3870 5 %RANDOM
Rwork0.227 ---
obs0.228 73031 76.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22980 0 0 138 23118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02123452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.92731948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68552972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94323.3461088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.179153548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.49815188
X-RAY DIFFRACTIONr_chiral_restr0.0710.23492
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218352
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.212641
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.216350
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.937515120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.169523840
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.737.59414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.70138108
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
11A3153medium positional0.160.5
12C3153medium positional0.180.5
13E3153medium positional0.160.5
14G3153medium positional0.170.5
21B2587medium positional0.110.5
22D2587medium positional0.10.5
23F2587medium positional0.110.5
24H2587medium positional0.110.5
11A3153medium thermal0.112
12C3153medium thermal0.12
13E3153medium thermal0.112
14G3153medium thermal0.12
21B2587medium thermal0.052
22D2587medium thermal0.042
23F2587medium thermal0.062
24H2587medium thermal0.042
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 126
Rwork0.34 2426

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