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- PDB-6a50: structure of benzoylformate decarboxylases in complex with cofact... -

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Basic information

Entry
Database: PDB / ID: 6a50
Titlestructure of benzoylformate decarboxylases in complex with cofactor TPP
Componentsbenzoylformate decarboxylases
KeywordsLYASE / ThDP / Glycolaldehyde Synthase
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuo, Y. / Wang, S. / Nie, Y. / Li, S.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesZDRW-ZS-2016 China
National Basic Research Program of China (973 Program)2015CB755704 China
CitationJournal: Nat Commun / Year: 2019
Title: A Synthetic Pathway for Acetyl-Coenzyme A Biosynthesis
Authors: Lu, X. / Liu, Y. / Yang, Y. / Wang, S. / Wang, Q. / Wang, X. / Yan, Z. / Cheng, J. / Liu, C. / Yang, X. / Luo, H. / Yang, S. / Gou, J. / Ye, L. / Lu, L. / Zhang, Z. / Guo, Y. / Nie, Y. / ...Authors: Lu, X. / Liu, Y. / Yang, Y. / Wang, S. / Wang, Q. / Wang, X. / Yan, Z. / Cheng, J. / Liu, C. / Yang, X. / Luo, H. / Yang, S. / Gou, J. / Ye, L. / Lu, L. / Zhang, Z. / Guo, Y. / Nie, Y. / Lin, J. / Li, S. / Cai, T. / Ma, H. / Wang, W. / Liu, Y. / Li, Y. / Jiang, H. / Tian, C.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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.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.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: benzoylformate decarboxylases
B: benzoylformate decarboxylases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2507
Polymers117,3272
Non-polymers9245
Water18,0331001
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-79 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.889, 124.392, 97.758
Angle α, β, γ (deg.)90.00, 122.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1065-

HOH

21A-1181-

HOH

31B-1067-

HOH

41B-1167-

HOH

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Components

#1: Protein benzoylformate decarboxylases


Mass: 58663.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: benzoylformate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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.: 1001 / 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: 46.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289.15 K / Method: liquid diffusion
Details: 0.2M calcium acetate, 0.1M HEPES (pH 7.5) and 40%(w/v) polyethylene glycol (PEG) 400

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Data collection

DiffractionMean temperature: 98.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→82.59 Å / Num. obs: 97121 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.53 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 0.956 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.60.72647780.8260.3010.7870.96598.7
1.83-1.866.70.69448370.8660.2850.750.97899
1.86-1.96.80.58948350.9060.2410.6370.96699
1.9-1.946.90.51248360.9240.2090.5540.9899.1
1.94-1.986.80.45148280.9340.1850.4880.99399.3
1.98-2.036.50.38448480.9460.1620.4171.01499.4
2.03-2.086.40.32348210.9570.1370.3511.01799.3
2.08-2.137.10.27548270.9720.110.2971.02399.4
2.13-2.27.10.22948980.9790.0920.2471.03799.5
2.2-2.2770.19448250.9840.0790.211.04399.6
2.27-2.356.90.16348250.9880.0670.1761.03699.6
2.35-2.446.60.14548770.9880.0610.1581.04499.8
2.44-2.556.50.11948690.9910.050.131.05299.5
2.55-2.697.10.10248630.9940.0410.111.02299.7
2.69-2.867.10.08948470.9950.0360.0960.99999.5
2.86-3.086.90.07148870.9960.0290.0770.954100
3.08-3.396.60.05549020.9970.0230.060.9199.5
3.39-3.887.20.04549010.9980.0180.0480.839100
3.88-4.886.60.03648700.9980.0150.0390.70699.4
4.88-506.90.03349470.9990.0130.0350.55899.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFD

1bfd


Resolution: 1.8→82.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.821 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.102
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17706 4969 5.1 %RANDOM
Rwork0.15904 ---
obs0.15997 92088 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20.04 Å2
2---0.28 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→82.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 55 1001 8958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.97111179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87251056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08724.327342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.051151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5341548
X-RAY DIFFRACTIONr_chiral_restr0.0820.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226334
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4551.6224224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8232.4295280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5711.7183952
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.61715.11613965
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 394 -
Rwork0.213 6574 -
obs--96.27 %
Refinement TLS params.Method: refined / Origin x: -32.439 Å / Origin y: -24.616 Å / Origin z: 17.353 Å
111213212223313233
T0.0024 Å20.0009 Å20 Å2-0.0176 Å20.0146 Å2--0.0189 Å2
L0.0639 °2-0.0051 °2-0.0003 °2-0.0796 °2-0.0188 °2--0.1759 °2
S0.0012 Å °0.0075 Å °-0.0002 Å °-0.0077 Å °-0.0192 Å °-0.0244 Å °0.0055 Å °0.0427 Å °0.018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 527
2X-RAY DIFFRACTION1A601 - 602

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