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- PDB-4wxy: PLPS (inactive glutaminase mutant) co-crystallized with glutamine... -

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Basic information

Entry
Database: PDB / ID: 4wxy
TitlePLPS (inactive glutaminase mutant) co-crystallized with glutamine and R5P.
Components
  • Glutamine amidotransferase subunit PdxT
  • Pyridoxal biosynthesis lyase PdxS
KeywordsTRANSFERASE / beta/alpha barrel / glutamine amidotransferase / vitamin b6 / pyridoxal 5-phosphate
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine catabolic process / glutaminase / glutaminase activity
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. ...Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxT / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSmith, J.L. / Smith, A.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase.
Authors: Smith, A.M. / Brown, W.C. / Harms, E. / Smith, J.L.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Nov 27, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _citation.title ..._citation.journal_id_CSD / _citation.title / _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 / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
G: Pyridoxal biosynthesis lyase PdxS
I: Pyridoxal biosynthesis lyase PdxS
K: Pyridoxal biosynthesis lyase PdxS
B: Glutamine amidotransferase subunit PdxT
D: Glutamine amidotransferase subunit PdxT
F: Glutamine amidotransferase subunit PdxT
H: Glutamine amidotransferase subunit PdxT
J: Glutamine amidotransferase subunit PdxT
L: Glutamine amidotransferase subunit PdxT


Theoretical massNumber of molelcules
Total (without water)348,07512
Polymers348,07512
Non-polymers00
Water4,738263
1
A: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
G: Pyridoxal biosynthesis lyase PdxS
I: Pyridoxal biosynthesis lyase PdxS
K: Pyridoxal biosynthesis lyase PdxS
B: Glutamine amidotransferase subunit PdxT
D: Glutamine amidotransferase subunit PdxT
F: Glutamine amidotransferase subunit PdxT
H: Glutamine amidotransferase subunit PdxT
J: Glutamine amidotransferase subunit PdxT
L: Glutamine amidotransferase subunit PdxT

A: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
G: Pyridoxal biosynthesis lyase PdxS
I: Pyridoxal biosynthesis lyase PdxS
K: Pyridoxal biosynthesis lyase PdxS
B: Glutamine amidotransferase subunit PdxT
D: Glutamine amidotransferase subunit PdxT
F: Glutamine amidotransferase subunit PdxT
H: Glutamine amidotransferase subunit PdxT
J: Glutamine amidotransferase subunit PdxT
L: Glutamine amidotransferase subunit PdxT


Theoretical massNumber of molelcules
Total (without water)696,15124
Polymers696,15124
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area81750 Å2
ΔGint-208 kcal/mol
Surface area174010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.023, 249.138, 179.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
31C
41E
51I
61K
12B
22D
32F
42H
52J
62L
13G
23A
33C
43E
53I
63K
14G
24A
34C
44E
54I
64K
15G
25A
35C
45E
55I
65K

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 80
2111G1 - 80
3111C1 - 80
4111E1 - 80
5111I1 - 80
6111K1 - 80
1121B1 - 192
2121D1 - 192
3121F1 - 192
4121H1 - 192
5121J1 - 192
6121L1 - 192
1131G261 - 290
2131A261 - 290
3131C261 - 290
4131E261 - 290
5131I261 - 290
6131K261 - 290
1141G82 - 260
2141A82 - 260
3141C82 - 260
4141E82 - 260
5141I82 - 260
6141K82 - 260
1151G81
2151A81
3151C81
4151E81
5151I81
6151K81

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.468957, -0.868749, -0.159229), (-0.868948, -0.486099, 0.09294), (-0.158142, 0.094777, -0.982857)55.62999, 79.846939, 82.629097
3given(-0.508213, -0.859043, -0.061347), (-0.85986, 0.502097, 0.092414), (-0.048585, 0.099716, -0.993829)51.00745, 23.78647, 83.690331
4given(0.498965, 0.865538, 0.043329), (-0.861684, 0.490171, 0.131274), (0.092384, -0.102837, 0.990399)-50.352211, 23.37768, 5.30545
5given(-0.478392, 0.859713, 0.178982), (-0.852962, -0.503381, 0.138073), (0.2088, -0.086612, 0.974116)-56.084919, 78.142647, 5.34972
6given(0.967426, 0.000725, -0.253153), (-0.001033, -0.999976, -0.006811), (-0.253152, 0.006851, -0.967402)11.17056, 112.297989, 87.64756
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Pyridoxal biosynthesis lyase PdxS


Mass: 33044.906 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: pdxS, GK0011 / Plasmid: pETTEV281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5L3Y2, Lyases
#2: Protein
Glutamine amidotransferase subunit PdxT / / Glutamine amidotransferase glutaminase subunit PdxT


Mass: 24967.656 Da / Num. of mol.: 6 / Mutation: H169N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: pdxT, GK0012 / Plasmid: plasmid / Details (production host): pETEV281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5L3Y1, EC: 2.6.-.-
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, Na malonate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2009 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.0331
ReflectionResolution: 2.7→50 Å / Num. obs: 86337 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Χ2: 1.081 / Net I/av σ(I): 10.091 / Net I/σ(I): 9.3 / Num. measured all: 284117
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.753.10.68742791.31598.9
2.75-2.83.10.60142791.2499.3
2.8-2.853.10.5643111.26299.3
2.85-2.913.20.46442951.21699.4
2.91-2.973.20.43843021.2599.6
2.97-3.043.20.38142971.2699.5
3.04-3.123.20.28243241.20399.5
3.12-3.23.20.25143261.17499.4
3.2-3.33.30.20842731.19399.4
3.3-3.43.30.16443301.13499.4
3.4-3.523.40.13843261.08399.2
3.52-3.663.40.11143071.04299.3
3.66-3.833.40.10543161.21499.1
3.83-4.033.40.08843231.06798.8
4.03-4.293.40.08343091.0398.9
4.29-4.623.40.08443241.25698.6
4.62-5.083.40.06543210.88898.4
5.08-5.813.40.0643160.74298.1
5.81-7.323.40.05343540.67197.7
7.32-503.30.04444250.52695.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2651 / WRfactor Rwork: 0.2137 / FOM work R set: 0.7896 / SU B: 15.262 / SU ML: 0.305 / SU Rfree: 0.3693 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 4323 5 %RANDOM
Rwork0.2091 81715 --
obs0.2115 81715 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.32 Å2 / Biso mean: 59.18 Å2 / Biso min: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2---1.03 Å20 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21904 0 0 263 22167
Biso mean---40.52 -
Num. residues----2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922202
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222027
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.98229918
X-RAY DIFFRACTIONr_angle_other_deg0.905350523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57752867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13223.522954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.161153897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91315204
X-RAY DIFFRACTIONr_chiral_restr0.0670.23405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225169
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024799
X-RAY DIFFRACTIONr_mcbond_it4.2315.6711510
X-RAY DIFFRACTIONr_mcbond_other4.235.6711509
X-RAY DIFFRACTIONr_mcangle_it6.5288.49514363
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A11296.31
12G11297.09
13C11295.9
14E11296.52
15I11296.7
16K11296.48
21B28999.64
22D28997.54
23F289910.95
24H28998.97
25J28997.58
26L28997.65
31G4668.38
32A46612.76
33C4667.93
34E46611.09
35I46611.73
36K4669.74
41G27304.83
42A27304.75
43C27305.48
44E27304.33
45I27304.85
46K27305.39
51G397.67
52A394.91
53C394.58
54E397.38
55I397.75
56K397.5
LS refinement shellResolution: 2.692→2.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 309 -
Rwork0.287 5761 -
all-6070 -
obs--94.46 %

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