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- PDB-3m5u: Crystal Structure of Phosphoserine Aminotransferase from Campylob... -

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Basic information

Entry
Database: PDB / ID: 3m5u
TitleCrystal Structure of Phosphoserine Aminotransferase from Campylobacter jejuni
ComponentsPhosphoserine aminotransferase
KeywordsTRANSFERASE / alpha-beta half sandwich / CSGID / Amino-acid biosynthesis / Aminotransferase / Cytoplasm / Pyridoxal phosphate / Pyridoxine biosynthesis / Serine biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / pyridoxine biosynthetic process / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / 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 ...Phosphoserine aminotransferase / 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
Phosphoserine aminotransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.152 Å
AuthorsKim, Y. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Phosphoserine Aminotransferase from Campylobacter jejuni
Authors: Kim, Y. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2195
Polymers82,7362
Non-polymers4833
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-16 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.738, 105.865, 70.009
Angle α, β, γ (deg.)90.00, 99.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoserine aminotransferase / Phosphohydroxythreonine aminotransferase / PSAT


Mass: 41368.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0326, serC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PIH3, phosphoserine transaminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M tri-Lithium Citrate 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 21, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 42606 / Num. obs: 42606 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 28.64 Å2 / Rsym value: 0.104 / Net I/σ(I): 10.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.94 / Num. unique all: 2106 / Rsym value: 0.541 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.152→34.857 Å / SU ML: 0.28 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2141 5.05 %random
Rwork0.169 ---
all0.172 42380 --
obs0.172 42380 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.444 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.3186 Å2-0 Å23.7377 Å2
2---4.7457 Å20 Å2
3----6.5729 Å2
Refinement stepCycle: LAST / Resolution: 2.152→34.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 30 428 6191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135884
X-RAY DIFFRACTIONf_angle_d1.3557928
X-RAY DIFFRACTIONf_dihedral_angle_d18.8212171
X-RAY DIFFRACTIONf_chiral_restr0.088848
X-RAY DIFFRACTIONf_plane_restr0.0051028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1517-2.22860.28282230.2293869419296
2.2286-2.31780.27412150.20973991420699
2.3178-2.42330.27531910.20740494240100
2.4233-2.5510.25512190.19840174236100
2.551-2.71070.2232180.17940464264100
2.7107-2.920.23952010.183440624263100
2.92-3.21360.26622250.181340174242100
3.2136-3.67820.19512070.153140794286100
3.6782-4.63240.18572210.132340544275100
4.6324-34.86140.17472210.15234055427699
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)
10.4578-0.00890.20250.89130.06070.36710.00530.01720.03870.0619-0.04840.06660.14220.01510.0390.0533-0.00220.02190.0240.00350.04234.73821.598659.732
20.40380.0252-0.26491.1521-0.41890.41080.0446-0.0447-0.03120.0195-0.03150.0416-0.1210.0179-0.01010.08490.0049-0.00650.08750.00590.06937.380127.819640.8395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 362
2X-RAY DIFFRACTION2chain BB1 - 361

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