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- PDB-4azk: Structural basis of L-phosphoserine binding to Bacillus alcalophi... -

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Basic information

Entry
Database: PDB / ID: 4azk
TitleStructural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase
ComponentsPHOSPHOSERINE AMINOTRANSFERASE
KeywordsTRANSFERASE / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesBACILLUS ALCALOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.595 Å
AuthorsBattula, P. / Dubnovitsky, A.P. / Papageorgiou, A.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase
Authors: Battula, P. / Dubnovitsky, A.P. / Papageorgiou, A.C.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _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

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Assembly

Deposited unit
A: PHOSPHOSERINE AMINOTRANSFERASE
B: PHOSPHOSERINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0526
Polymers80,4872
Non-polymers5654
Water19,9251106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-58.5 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.598, 136.599, 152.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE / PHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE / PSAT


Mass: 40243.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE BETWEEN PLP AND LYS196 / Source: (gene. exp.) BACILLUS ALCALOPHILUS (bacteria) / Plasmid: PBALC-PSAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RME2, phosphoserine transaminase
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL METHIONINE IS CLEAVED OFF IN THE MATURE PROTEIN

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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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 8.5
Details: 1.4 M TRI-SODIUM CITRATE DIHYDRATE, TRI-HCL 0.1 M, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 144217 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.65 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AZJ

4azj


Resolution: 1.595→28.318 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 15.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1705 7292 5.1 %
Rwork0.1535 --
obs0.1544 144142 99.17 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.656 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.562 Å20 Å20 Å2
2---0.638 Å20 Å2
3----0.9239 Å2
Refinement stepCycle: LAST / Resolution: 1.595→28.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 32 1106 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125890
X-RAY DIFFRACTIONf_angle_d1.4598011
X-RAY DIFFRACTIONf_dihedral_angle_d14.3552229
X-RAY DIFFRACTIONf_chiral_restr0.084895
X-RAY DIFFRACTIONf_plane_restr0.0071048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5952-1.61330.22192170.20824141X-RAY DIFFRACTION91
1.6133-1.63230.25582370.22124500X-RAY DIFFRACTION98
1.6323-1.65220.2472180.2234494X-RAY DIFFRACTION98
1.6522-1.67310.25172520.21844474X-RAY DIFFRACTION99
1.6731-1.69510.25852320.20824562X-RAY DIFFRACTION99
1.6951-1.71830.23562420.20434538X-RAY DIFFRACTION100
1.7183-1.74290.21772470.19854523X-RAY DIFFRACTION100
1.7429-1.76890.2262450.18664560X-RAY DIFFRACTION100
1.7689-1.79650.20722420.18734612X-RAY DIFFRACTION100
1.7965-1.8260.2112500.18114527X-RAY DIFFRACTION100
1.826-1.85740.22092150.18344584X-RAY DIFFRACTION100
1.8574-1.89120.21962590.18684537X-RAY DIFFRACTION100
1.8912-1.92760.21432630.18984569X-RAY DIFFRACTION100
1.9276-1.96690.1872720.16124536X-RAY DIFFRACTION100
1.9669-2.00970.16692390.15164584X-RAY DIFFRACTION100
2.0097-2.05640.18662390.14914600X-RAY DIFFRACTION100
2.0564-2.10780.16422440.14934597X-RAY DIFFRACTION100
2.1078-2.16480.162480.14174544X-RAY DIFFRACTION100
2.1648-2.22850.17472270.1544608X-RAY DIFFRACTION100
2.2285-2.30040.18312380.15544601X-RAY DIFFRACTION100
2.3004-2.38250.16522520.14734558X-RAY DIFFRACTION100
2.3825-2.47790.15522580.13944601X-RAY DIFFRACTION100
2.4779-2.59060.15332610.144566X-RAY DIFFRACTION100
2.5906-2.72710.15012560.13984609X-RAY DIFFRACTION100
2.7271-2.89780.14622220.14134629X-RAY DIFFRACTION100
2.8978-3.12120.16622430.1444611X-RAY DIFFRACTION99
3.1212-3.43490.15592250.14034654X-RAY DIFFRACTION99
3.4349-3.93080.13452610.12734596X-RAY DIFFRACTION99
3.9308-4.94810.12582330.11384631X-RAY DIFFRACTION99
4.9481-28.32270.16942550.1744704X-RAY DIFFRACTION97

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