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- PDB-6hbv: Structure of PLP internal aldimine form of Sphingopyxis sp. MTA14... -

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Basic information

Entry
Database: PDB / ID: 6hbv
TitleStructure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
ComponentsAminopentol aminotransferase
KeywordsTRANSFERASE / aminotransferase / PLP / fumonisin
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminopentol aminotransferase
Similarity search - Component
Biological speciesSphingopyxis macrogoltabida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCampopiano, D.J. / Serpico, A. / Marles-Wright, J.
CitationJournal: To Be Published
Title: Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein
Authors: Campopiano, D.J. / Serpico, A. / Marles-Wright, J.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.2Aug 7, 2024Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_set_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopentol aminotransferase
B: Aminopentol aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6787
Polymers96,6632
Non-polymers1,0155
Water17,006944
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-60 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.254, 103.903, 65.326
Angle α, β, γ (deg.)90.00, 109.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminopentol aminotransferase


Mass: 48331.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis macrogoltabida (bacteria) / Gene: fumI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D2D3B2, Transferases; Transferring nitrogenous groups; Transaminases
#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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30 % w/v Polyactulate 2100, sodium salt 0.2 M Ammonium Sulfate 0.1 M Hepes pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2017
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→46.86 Å / Num. obs: 95210 / % possible obs: 99.74 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06215 / Rpim(I) all: 0.03715 / Rrim(I) all: 0.07264 / Net I/σ(I): 13.95
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5554 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 9539 / CC1/2: 0.849 / Rpim(I) all: 0.3371 / Rrim(I) all: 0.6521 / % possible all: 99.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bs8

3bs8


Resolution: 1.65→46.91 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.347 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17414 4764 5 %RANDOM
Rwork0.14281 ---
obs0.14437 91044 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.583 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-0.76 Å2
2--3.69 Å20 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.65→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 63 944 7393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0146652
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175738
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6659049
X-RAY DIFFRACTIONr_angle_other_deg1.0621.6413419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.155.49868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7220.58362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5421558
X-RAY DIFFRACTIONr_chiral_restr0.0880.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.028336
X-RAY DIFFRACTIONr_gen_planes_other00.021318
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_it1.3871.8673313
X-RAY DIFFRACTIONr_mcbond_other1.3761.8663312
X-RAY DIFFRACTIONr_mcangle_it1.8642.7954142
X-RAY DIFFRACTIONr_mcangle_other1.8642.7964143
X-RAY DIFFRACTIONr_scbond_it2.7212.1713339
X-RAY DIFFRACTIONr_scbond_other2.7212.1713340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.143.144903
X-RAY DIFFRACTIONr_long_range_B_refined5.59824.3588105
X-RAY DIFFRACTIONr_long_range_B_other5.26123.1337747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.645→1.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 355 -
Rwork0.251 6507 -
obs--96.81 %

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