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- PDB-4dq6: Crystal structure of PLP-bound putative aminotransferase from Clo... -

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Basic information

Entry
Database: PDB / ID: 4dq6
TitleCrystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630
ComponentsPutative pyridoxal phosphate-dependent transferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / 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: 1.5 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
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 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)90,7747
Polymers90,1732
Non-polymers6015
Water18,5911032
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-51 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.426, 56.094, 85.275
Angle α, β, γ (deg.)90.000, 99.330, 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein: 0.3M NaCl, 10mM Hepes pH 7.5. Precipitant: 25%PEG 2K MME, 0.2M Na Chloride, 0.1M Na Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 119055 / Num. obs: 118460 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Χ2: 1.188 / Net I/σ(I): 21.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.5-1.533.40.4932.355590.82293.6
1.53-1.553.60.45457500.85397.9
1.55-1.583.80.40558610.85699.3
1.58-1.623.90.38859330.88299.9
1.62-1.6540.35559510.89399.8
1.65-1.6940.29758700.93699.9
1.69-1.734.10.27259340.92999.9
1.73-1.784.10.22159110.96199.9
1.78-1.834.10.18759570.99999.9
1.83-1.894.10.15559261.05199.9
1.89-1.964.10.12359191.12499.9
1.96-2.044.10.10459241.18100
2.04-2.134.10.08759541.241100
2.13-2.244.20.07659581.284100
2.24-2.384.20.07159611.355100
2.38-2.564.20.06759741.499100
2.56-2.824.20.06659581.743100
2.82-3.234.20.05759731.829100
3.23-4.074.10.04560381.515100
4.07-504.10.04861491.49599.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DGT

4dgt


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1863 / WRfactor Rwork: 0.1522 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8617 / SU B: 2.993 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0698 / SU Rfree: 0.0731 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 5910 5 %RANDOM
Rwork0.1525 ---
all0.1542 118680 --
obs0.1542 118099 99.51 %-
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: 63.63 Å2 / Biso mean: 22.3319 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-1.03 Å2
2---0.65 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 33 1032 7323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026527
X-RAY DIFFRACTIONr_bond_other_d0.0010.024421
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9678857
X-RAY DIFFRACTIONr_angle_other_deg1.686310899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53825.563311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.357151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3531525
X-RAY DIFFRACTIONr_chiral_restr0.1120.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021247
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 439 -
Rwork0.251 7595 -
all-8034 -
obs-7595 94.86 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70440.25050.05660.2259-0.13540.1136-0.00780.3265-0.1948-0.04290.0138-0.02810.02210.0359-0.00610.06590.00160.00330.1041-0.04660.02522.63219.29248.446
21.68840.20150.1570.3381-0.07430.07270.0157-0.21320.17310.0427-0.02910.02820.0058-0.0240.01350.0801-0.00310.01330.0713-0.02920.0211-4.633.14170.101
31.29490.0754-0.03030.3745-0.06290.1876-0.01570.1501-0.18280.00430.00930.04380.03360.00180.00640.0566-0.0030.01020.0424-0.02550.0359-11.51516.5956.129
41.29680.35130.0970.29650.01710.0646-0.02890.35140.1961-0.0487-0.00430.0419-0.0097-0.00310.03320.07860.00740.00960.16620.04550.039323.3434.51148.575
51.24990.12040.14680.2430.07510.22460.0388-0.0665-0.17170.0401-0.0132-0.0284-0.0033-0.007-0.02560.0763-0.0023-0.00090.03240.01220.02530.54920.65370.115
61.15060.16280.10950.40370.08350.2832-0.02420.21280.1203-0.00460.0129-0.0465-0.05090.02690.01120.063-0.00180.00530.05580.02880.025837.62737.07856.123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 61
2X-RAY DIFFRACTION2A62 - 266
3X-RAY DIFFRACTION3A267 - 388
4X-RAY DIFFRACTION4B1 - 61
5X-RAY DIFFRACTION5B62 - 266
6X-RAY DIFFRACTION6B267 - 388

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