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- PDB-4xk1: Crystal Structure of a Phosphoserine/phosphohydroxythreonine Amin... -

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Basic information

Entry
Database: PDB / ID: 4xk1
TitleCrystal Structure of a Phosphoserine/phosphohydroxythreonine Aminotransferase (PSAT) from Pseudomonas aeruginosa with cofactor Pyridoxal Phosphate and bound Glutamate
ComponentsPhosphoserine aminotransferasePhosphoserine transaminase
KeywordsTRANSFERASE / SSGCID / Pseudomonas aeruginosa / Phosphoserine aminotransferase / Phosphohydroxythreonine aminotransferase / PSAT / Aminotransferase class-V / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
FORMIC ACID / GLUTAMIC ACID / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Phosphoserine/phosphohydroxythreonine Aminotransferase (PSAT) from Pseudomonas aeruginosa with cofactor Pyridoxal Phosphate and bound Glutamate
Authors: SSGCID / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 2.0Oct 11, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / reflns_shell / software / struct_keywords
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,7846
Polymers82,4992
Non-polymers2854
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-19 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.220, 72.220, 268.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is a dimer, same as the asymmetric unit

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Components

#1: Protein Phosphoserine aminotransferase / Phosphoserine transaminase / Phosphohydroxythreonine aminotransferase / PSAT


Mass: 41249.352 Da / Num. of mol.: 2 / Fragment: PsaeA.00980.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: serC, PA3167 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZ66, phosphoserine transaminase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PsaeA.00980.a.B1.PW37585 at 22 mg/ml mixed 1:1 with Morpheus(g9): 10% PEG-20,000, 20% PEG-MME-550, 0.1M bicine/ trizma base, pH=8.5, 0.02M each sodium formate, ammonium acetate, trisodium ...Details: PsaeA.00980.a.B1.PW37585 at 22 mg/ml mixed 1:1 with Morpheus(g9): 10% PEG-20,000, 20% PEG-MME-550, 0.1M bicine/ trizma base, pH=8.5, 0.02M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 45360 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 42.66 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Χ2: 1 / Net I/σ(I): 26.24 / Num. measured all: 328897
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.217.40.8870.5433.5424398329132940.584100
2.21-2.270.9350.4174.6123866323732370.449100
2.27-2.330.9650.3165.9223225314231420.339100
2.33-2.40.9740.2617.2322459303630360.28100
2.4-2.480.9860.2029.2821827294529450.217100
2.48-2.570.9890.16311.2921131285728570.175100
2.57-2.670.9950.12414.3820346276127610.133100
2.67-2.780.9960.0981819778268726870.106100
2.78-2.90.9970.07822.3218832255925580.084100
2.9-3.040.9980.06626.2517830243324330.07100
3.04-3.210.9990.0533.7917174234723460.054100
3.21-3.40.9990.0441.3216069221522150.043100
3.4-3.630.9990.03447.5415085210821080.037100
3.63-3.930.9990.0354.9913845195319530.032100
3.93-4.30.9990.02957.7712779182418210.03199.8
4.3-4.810.9990.02662.1511612166716700.028100
4.81-5.5510.0246210254146614650.02699.9
5.55-6.810.02161.348723125912590.023100
6.8-9.620.9990.01864.386670101710160.0299.9
9.620.9990.01860.4529946095570.01991.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.741 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 2199 4.98 %
Rwork0.1793 41983 -
obs0.1813 44182 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.48 Å2 / Biso mean: 57.2411 Å2 / Biso min: 25.73 Å2
Refinement stepCycle: final / Resolution: 2.15→40.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 19 233 5608
Biso mean--76.26 50.66 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085518
X-RAY DIFFRACTIONf_angle_d1.1117522
X-RAY DIFFRACTIONf_chiral_restr0.045826
X-RAY DIFFRACTIONf_plane_restr0.005983
X-RAY DIFFRACTIONf_dihedral_angle_d13.1681917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1501-2.19680.28051120.22642430254291
2.1968-2.24790.30981260.21622453257993
2.2479-2.30410.24841450.20852445259093
2.3041-2.36640.31581230.20842541266495
2.3664-2.4360.24931410.20362516265796
2.436-2.51470.25761460.19852574272097
2.5147-2.60450.23391260.19712621274798
2.6045-2.70880.23081850.19152561274699
2.7088-2.8320.27761130.20322672278599
2.832-2.98130.2711360.21252682281899
2.9813-3.1680.2481360.21252660279699
3.168-3.41250.22841490.199326922841100
3.4125-3.75570.2361380.174727222860100
3.7557-4.29870.17521400.150627212861100
4.2987-5.41380.17061490.14327832932100
5.4138-40.74850.19721340.172910304498
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)
15.3628-2.79155.71063.9769-4.00546.52180.09140.52-0.30450.9662-0.11250.1214-0.55970.71420.04120.60350.0413-0.00440.34660.01920.272915.796512.315515.6232
21.53460.3816-0.57942.448-1.73632.42150.09990.285-0.0096-0.08240.05450.1876-0.02060.0737-0.17450.54240.1039-0.08540.3208-0.01860.2903-3.081710.610711.7674
38.0231-1.19641.82293.6071-0.20972.5067-0.2883-0.64490.16760.17880.33820.3115-0.247-0.3051-0.0030.60870.12260.03660.2410.04140.3647-5.86390.011836.7023
44.2078-1.07860.21320.8023-0.1811.05980.3063-0.0318-0.6051-0.0627-0.10630.18050.3102-0.0244-0.18230.63090.0783-0.0380.19460.00960.4439-0.6239-8.617533.3125
56.0086-0.9806-0.77730.823-0.51642.9947-0.01070.18510.0045-0.1655-0.04060.07510.0767-0.00480.06490.49990.0693-0.02730.2056-0.01710.3-5.26152.560321.2244
62.8855-1.03772.14172.1556-1.60884.02940.16550.2687-0.2153-0.1082-0.2112-0.00840.22840.63210.0360.45430.08110.0410.304-0.02150.285113.36480.623421.312
73.5819-0.1842.2321.90260.49115.6461-0.08260.17650.3663-0.2099-0.14950.0518-1.55130.910.12290.7912-0.1310.11710.50220.05020.386922.8776.968931.7005
88.31871.56913.98474.55431.84526.86940.38180.16810.2340.06740.093-0.4526-0.48262.1543-0.51580.4904-0.0760.090.7964-0.04650.433331.72641.226926.8297
94.4507-1.6207-2.36897.2637-0.26885.27420.4581-0.1150.2678-0.0811-0.478-0.4418-0.71920.9591-00.6486-0.1501-0.01980.4207-0.08150.35799.820225.529815.8086
101.918-0.90060.30132.05290.15371.2819-0.0701-0.08780.02780.21160.1690.3033-0.5647-0.0326-0.09360.80660.12870.03220.2832-0.02060.4634-13.877329.720928.3381
114.1076-1.01641.08032.8319-0.79611.3285-0.07840.31410.4512-0.23970.10770.0891-0.5221-0.05790.03060.98820.01380.01580.36940.03780.3607-7.131837.501114.1675
125.0974-0.05173.28456.01910.21682.158-0.47810.9210.24-0.93410.02050.36040.91420.50.39651.416-0.17240.18561.0368-0.18010.5535-14.03431.2046-2.6745
134.6195-0.1423.34311.70571.47153.8739-0.59070.77030.4925-0.25760.4637-0.1642-0.7393-0.18540.11771.0101-0.16430.06330.57250.11250.5421-6.908939.61174.7359
142-6.63395.71135.479-1.89034.7026-0.5646-1.4662.47510.32830.1922-1.8777-0.62341.70840.43460.9208-0.2263-0.34420.87590.06140.802721.749614.600216.3765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 113 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 173 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 232 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 233 through 305 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 342 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 343 through 360 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 44 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 232 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 233 through 305 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 306 through 332 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 333 through 352 )B0
14X-RAY DIFFRACTION14chain 'D' and (resid 401 through 401 )D0

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