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- PDB-1bt4: PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALK... -

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Basic information

Entry
Database: PDB / ID: 1bt4
TitlePHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS SUBSP. ALKALOPHILUS
ComponentsPhosphoserine aminotransferasePhosphoserine transaminase
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHOSERINE / ALKALIPHILIC
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 circulans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHester, G. / Luong, T.N. / Moser, M. / Jansonius, J.N.
Citation
Journal: To be Published
Title: The Crystal Structure of Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus
Authors: Hester, G. / Luong, T.N. / Moser, M. / Jansonius, J.N.
#1: Journal: Protein Sci. / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus
Authors: Moser, M. / Muller, R. / Battchikova, N. / Koivulehto, M. / Korpela, T. / Jansonius, J.N.
#2: Journal: Biochim.Biophys.Acta / Year: 1996
Title: Phosphoserine Aminotransferase from Bacillus Circulans Subsp. Alkalophilus: Purification, Gene Cloning and Sequencing
Authors: Battchikova, N. / Himanen, J.-P. / Ahjolahti, M. / Korpela, T.
History
DepositionSep 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 10, 2016Group: Database references / Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 9, 2023Group: 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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0822
Polymers39,8351
Non-polymers2471
Water1,76598
1
A: Phosphoserine aminotransferase
hetero molecules

A: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1644
Polymers79,6702
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5730 Å2
ΔGint-25 kcal/mol
Surface area27580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.323, 92.876, 45.499
Angle α, β, γ (deg.)90.00, 106.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphoserine aminotransferase / Phosphoserine transaminase / EC 2.6.1.52 TRANSFERASE / Phosphohydroxythreonine aminotransferase / PSAT


Mass: 39834.895 Da / Num. of mol.: 1 / Fragment: ONE COMPLETE SUBUNIT / Mutation: K3E / Source method: isolated from a natural source
Details: THE COFACTOR PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY LINKED TO THE SIDE CHAIN OF LYS 197
Source: (natural) Bacillus circulans (bacteria) / Variant: ALKALOPHILUS / Strain: subsp. alkalophilus / References: UniProt: Q59196, phosphoserine transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPLP MOLECULE IS COVALENTLY LINKED TO THE SIDE CHAIN OF LYS 197
Sequence detailsMET 1 IS CLEAVED OFF IN A POST-TRANSLATIONAL PROCESS

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growMethod: macroseeding / pH: 4.6
Details: CRYSTALLIZED AT ROOM TEMPERATURE FROM 0.1 M SODIUM ACETATE BUFFER, PH 4.6, 2-6% GLYCEROL, 2-4% PEG 20000, USING MACROSEEDING TECHNIQUES, macroseeding
Temp details: room temp

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.3 Å / Num. obs: 16466 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 7.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5 / Rsym value: 0.219 / % possible all: 96.4

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJN

1bjn


Resolution: 2.3→29.3 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 843 5.1 %RANDOM
Rwork0.184 ---
obs0.184 16466 99.4 %-
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-30 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 15 98 2913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.35 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.379 65 6.2 %
Rwork0.259 985 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PTOPHCSDX.P
X-RAY DIFFRACTION2PARAM19.SOTOP
X-RAY DIFFRACTION3PLP.PAR_OPLP.TOP_O

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