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- PDB-4dgt: Crystal structure of PLP-bound putative aminotransferase from Clo... -

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Basic information

Entry
Database: PDB / ID: 4dgt
TitleCrystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630 crystallized with magnesium formate
ComponentsPutative pyridoxal phosphate-dependent transferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / internal aldimine with pyridoxalphosphate
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / transferase activity
Similarity search - Function
Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShabalin, I.G. / Onopriyenko, O. / Kudritska, M. / Chruszcz, M. / Grimshaw, S. / Porebski, P.J. / Cooper, D.R. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: to be published
Title: Crystal structures of putative aminotransferase from Clostridium difficile 630
Authors: Shabalin, I.G. / Onopriyenko, O. / Kudritska, M. / Grimshaw, S. / Chruszcz, M. / Porebski, P.J. / Cooper, D.R. / Savchenko, A. / Anderson, W.F. / Minor, W.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pyridoxal phosphate-dependent transferase
B: Putative pyridoxal phosphate-dependent transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,02817
Polymers90,1732
Non-polymers85515
Water15,817878
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-102 kcal/mol
Surface area28260 Å2
MethodPISA
2
A: Putative pyridoxal phosphate-dependent transferase
hetero molecules

B: Putative pyridoxal phosphate-dependent transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,02817
Polymers90,1732
Non-polymers85515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3570 Å2
ΔGint-92 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.744, 55.624, 79.133
Angle α, β, γ (deg.)90.000, 91.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative pyridoxal phosphate-dependent transferase


Mass: 45086.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD2733, CD630_27330 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q183G9
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 1.92 Å3/Da / Density % sol: 35.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 3350, 2M Mg Formate, pH 7.0, vapor diffusion, hanging drop, temperature 20K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 99598 / Num. obs: 99100 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 19
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4608 / Rsym value: 0.407 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SwissModel generated model based on PDB ENTRY 3T32 structure
Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.755 / SU ML: 0.052 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 4947 5 %RANDOM
Rwork0.1475 ---
all0.1491 99489 --
obs0.1491 99012 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.62 Å2 / Biso mean: 17.2009 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.08 Å2
2---0.33 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6274 0 43 878 7195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026539
X-RAY DIFFRACTIONr_bond_other_d0.0030.024435
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9658866
X-RAY DIFFRACTIONr_angle_other_deg2.428310938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16825.556315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.837151227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7811526
X-RAY DIFFRACTIONr_chiral_restr0.1170.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021246
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 313 -
Rwork0.199 6537 -
all-6850 -
obs-6850 95.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6853-0.39580.12830.9512-0.01670.3263-0.00990.10760.1322-0.0855-0.00080.0912-0.0622-0.07580.01070.03030.0025-0.00670.09940.02780.040234.13712.9848.534
20.3935-0.0615-0.03150.0846-0.02040.24130.0132-0.0049-0.03450.0081-0.0026-0.00260.0210.0247-0.01060.00490.0058-0.00390.05330.00040.00534.951-6.62824.441
30.6030.11210.11120.48830.11360.7607-0.00950.04190.06790.0231-0.0038-0.0501-0.1050.01550.01330.0178-0.0054-0.00660.06540.01110.016748.01313.45314.691
40.6789-1.13520.71353.1123-0.99490.91310.05680.1593-0.0426-0.06940.0106-0.23170.10290.1627-0.06730.06450.0157-0.00790.1606-0.05960.10925.218-12.3028.043
50.5432-0.0496-0.03810.0652-0.00320.22460.0186-0.02290.04150.0065-0.00360.0009-0.0172-0.0204-0.01490.00290.00280.00280.0596-0.00210.00424.6216.54824.862
60.47170.0853-0.07630.26320.24521.1421-0.00490.0056-0.03950.0477-0.03510.0490.2585-0.06470.040.06-0.020.00530.0834-0.00760.0168-8.838-12.79814.212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 43
2X-RAY DIFFRACTION2A44 - 285
3X-RAY DIFFRACTION3A286 - 388
4X-RAY DIFFRACTION4B2 - 43
5X-RAY DIFFRACTION5B44 - 285
6X-RAY DIFFRACTION6B286 - 388

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