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- PDB-4q9d: X-ray structure of a putative thiamin diphosphate-dependent enzym... -

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Basic information

Entry
Database: PDB / ID: 4q9d
TitleX-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from Mycobacterium smegmatis
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / thiamin diphosphate-dependent decarboxylase
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
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 ...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
FORMIC ACID / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAndrews, F.H. / Horton, J.D. / Yoon, H.J. / Malik, A.M.K. / Logsdon, M.G. / Shin, D.H. / Kneen, M.M. / Suh, S.W. / McLeish, M.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes.
Authors: Andrews, F.H. / Horton, J.D. / Shin, D. / Yoon, H.J. / Logsdon, M.G. / Malik, A.M. / Rogers, M.P. / Kneen, M.M. / Suh, S.W. / McLeish, M.J.
History
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
B: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7768
Polymers116,5442
Non-polymers2336
Water16,340907
1
A: Benzoylformate decarboxylase
B: Benzoylformate decarboxylase
hetero molecules

A: Benzoylformate decarboxylase
B: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,55316
Polymers233,0874
Non-polymers46512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area22900 Å2
ΔGint-129 kcal/mol
Surface area63460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.162, 137.162, 337.057
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21A-882-

HOH

31A-1085-

HOH

41B-701-

HOH

51B-1172-

HOH

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Components

#1: Protein Benzoylformate decarboxylase


Mass: 58271.809 Da / Num. of mol.: 2 / Fragment: MsBFDC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1606, MSMEI_1567 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QSU7, benzoylformate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4 M NaFormate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 1308379 / Num. obs: 95599 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 46.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1308379 / Rsym value: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.899 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 4786 5.01 %random
Rwork0.1503 ---
obs0.1521 95438 99.97 %-
all-95467 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7762 0 14 907 8683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137962
X-RAY DIFFRACTIONf_angle_d1.30910912
X-RAY DIFFRACTIONf_dihedral_angle_d12.1552851
X-RAY DIFFRACTIONf_chiral_restr0.0871262
X-RAY DIFFRACTIONf_plane_restr0.0061435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.22520.25281460.18542962X-RAY DIFFRACTION100
2.2252-2.25130.26041600.17282978X-RAY DIFFRACTION100
2.2513-2.27880.22471560.16342964X-RAY DIFFRACTION100
2.2788-2.30760.19931700.16422945X-RAY DIFFRACTION100
2.3076-2.3380.22621510.16512982X-RAY DIFFRACTION100
2.338-2.370.19991560.1582989X-RAY DIFFRACTION100
2.37-2.40390.20181510.15312992X-RAY DIFFRACTION100
2.4039-2.43970.18641480.15592980X-RAY DIFFRACTION100
2.4397-2.47790.21211470.15422984X-RAY DIFFRACTION100
2.4779-2.51850.18261620.15452947X-RAY DIFFRACTION100
2.5185-2.56190.20081480.15623002X-RAY DIFFRACTION100
2.5619-2.60850.21491690.16172983X-RAY DIFFRACTION100
2.6085-2.65860.22131670.1622979X-RAY DIFFRACTION100
2.6586-2.71290.21541640.16942983X-RAY DIFFRACTION100
2.7129-2.77180.26061510.17433006X-RAY DIFFRACTION100
2.7718-2.83630.20281800.17682973X-RAY DIFFRACTION100
2.8363-2.90720.20891780.18052984X-RAY DIFFRACTION100
2.9072-2.98570.19871430.18063040X-RAY DIFFRACTION100
2.9857-3.07360.22581700.16922973X-RAY DIFFRACTION100
3.0736-3.17270.20941530.17563025X-RAY DIFFRACTION100
3.1727-3.2860.20761630.16443013X-RAY DIFFRACTION100
3.286-3.41750.18291440.14743048X-RAY DIFFRACTION100
3.4175-3.57290.17961660.14253014X-RAY DIFFRACTION100
3.5729-3.76110.14871440.1273059X-RAY DIFFRACTION100
3.7611-3.99640.15721450.12343070X-RAY DIFFRACTION100
3.9964-4.30450.17521400.12223104X-RAY DIFFRACTION100
4.3045-4.73690.13231630.11613082X-RAY DIFFRACTION100
4.7369-5.42030.15831820.12983103X-RAY DIFFRACTION100
5.4203-6.82130.19161950.15133127X-RAY DIFFRACTION100
6.8213-35.90360.14491740.16163361X-RAY DIFFRACTION100

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