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- PDB-6w6a: Crystal structure of a pyridoxine 5'-phosphate synthease from Ste... -

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Basic information

Entry
Database: PDB / ID: 6w6a
TitleCrystal structure of a pyridoxine 5'-phosphate synthease from Stenotrophomonas maltophilia K279a
ComponentsPyridoxine 5'-phosphate synthase
KeywordsLYASE / NIAID / National Institute of Allergy and Infectious Diseases / PLP synthesis / pyridoxine 5-phosphate phorpho lyase / transferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / cytoplasm
Similarity search - Function
Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ / Pyridoxine 5'-phosphate synthase / Pyridoxal phosphate biosynthesis protein PdxJ / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Pyridoxine 5'-phosphate synthase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a pyridoxine 5'-phosphate synthease from Stenotrophomonas maltophilia K279a
Authors: Edwards, T.E. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxine 5'-phosphate synthase
B: Pyridoxine 5'-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7134
Polymers54,5232
Non-polymers1902
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-27 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.780, 57.470, 71.770
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -1 through 1 and (name N...
21(chain B and ((resid -1 through 1 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMET(chain A and ((resid -1 through 1 and (name N...AA-1 - 17 - 9
12LEULEU(chain A and ((resid -1 through 1 and (name N...AA-1 - 2477 - 255
13LEULEU(chain A and ((resid -1 through 1 and (name N...AA-1 - 2477 - 255
14LEULEU(chain A and ((resid -1 through 1 and (name N...AA-1 - 2477 - 255
15LEULEU(chain A and ((resid -1 through 1 and (name N...AA-1 - 2477 - 255
21METMET(chain B and ((resid -1 through 1 and (name N...BB-1 - 17 - 9
22LEULEU(chain B and ((resid -1 through 1 and (name N...BB-4 - 2474 - 255
23LEULEU(chain B and ((resid -1 through 1 and (name N...BB-4 - 2474 - 255
24LEULEU(chain B and ((resid -1 through 1 and (name N...BB-4 - 2474 - 255
25LEULEU(chain B and ((resid -1 through 1 and (name N...BB-4 - 2474 - 255

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Components

#1: Protein Pyridoxine 5'-phosphate synthase / PNP synthase


Mass: 27261.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: pdxJ, Smlt0015 / Production host: Escherichia coli (E. coli)
References: UniProt: B2FT93, pyridoxine 5'-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: StmaA.01536.a.B1.PW38756 at 11.4 mg/mL with 3 mM PLP against Morpheus screen condition E1: 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MES/imidazole pH 6.5, 0.03 M each glycol (diethyleneglycol, ...Details: StmaA.01536.a.B1.PW38756 at 11.4 mg/mL with 3 mM PLP against Morpheus screen condition E1: 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MES/imidazole pH 6.5, 0.03 M each glycol (diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol)
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→45.61 Å / Num. obs: 27465 / % possible obs: 99.2 % / Redundancy: 3.726 % / Biso Wilson estimate: 54.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.075 / Χ2: 1.033 / Net I/σ(I): 12.01 / Num. measured all: 102338 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.513.8450.5352.347786204920250.910.62298.8
2.51-2.583.8230.4072.927462196019520.9450.47499.6
2.58-2.663.8360.3653.267377194719230.9480.42598.8
2.66-2.743.8180.2943.936952184418210.9710.34298.8
2.74-2.833.8250.2414.86889180718010.9790.28199.7
2.83-2.933.8090.18166627175617400.9880.21199.1
2.93-3.043.7750.1527.16353170216830.9920.17798.9
3.04-3.163.7590.1149.146213166016530.9930.13399.6
3.16-3.33.7270.0911.315699153715290.9970.10699.5
3.3-3.463.670.07613.555454150314860.9960.08998.9
3.46-3.653.6570.06914.45197143114210.9960.08199.3
3.65-3.873.5880.06416.724847136713510.9960.07698.8
3.87-4.143.6120.05120.344529126312540.9970.0699.3
4.14-4.473.6030.04124.274255118511810.9980.04999.7
4.47-4.93.6190.03725.93985110611010.9980.04399.5
4.9-5.483.6160.04125.1435879939920.9980.04899.9
5.48-6.333.6310.03725.8431958848800.9980.04499.5
6.33-7.753.6070.03227.2127057527500.9980.03799.7
7.75-10.963.6030.02531.2921265985900.9990.02998.7
10.96-45.613.3130.02330.7711003413320.9980.02897.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1.3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dlc

5dlc


Resolution: 2.45→45.61 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.28
RfactorNum. reflection% reflection
Rfree0.2335 1970 7.19 %
Rwork0.1951 --
obs0.1979 27392 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.17 Å2 / Biso mean: 65.4772 Å2 / Biso min: 32.73 Å2
Refinement stepCycle: final / Resolution: 2.45→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 10 68 3731
Biso mean--91.08 54.54 -
Num. residues----495
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2116X-RAY DIFFRACTION5.941TORSIONAL
12B2116X-RAY DIFFRACTION5.941TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.510.33921320.30071815194798
2.51-2.580.35361400.28531791193199
2.58-2.660.39651340.27821808194298
2.66-2.740.32621610.26671740190198
2.74-2.840.29521580.24431805196399
2.84-2.950.31171290.25411813194298
2.95-3.090.32531350.25751804193999
3.09-3.250.27681390.2471793193299
3.25-3.450.24821460.22141800194699
3.45-3.720.25791350.20881828196399
3.72-4.090.20331430.18131824196799
4.09-4.690.17951360.142118471983100
4.69-5.90.18381400.148518511991100
5.9-45.610.17141420.15131903204599
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)
15.81650.46832.31691.5151-0.48664.2856-0.09970.0082-0.1844-0.2020.5127-0.2702-0.01110.3799-0.54470.4038-0.02810.00570.44050.0280.4998-21.1908-2.96927.5812
24.2085-0.71050.27282.44020.0341.4946-0.06080.2896-0.0519-0.2623-0.0090.19320.04730.21920.03390.4192-0.0523-0.02340.42250.01740.3968-12.5862-2.07273.5306
35.87711.65880.13363.0675-0.26993.92850.3567-0.6709-0.7250.07210.0627-0.48640.3080.9828-0.33110.40530.0129-0.01390.7173-0.04150.4704-2.1103-4.381317.6341
42.70830.53530.79382.52620.02192.20520.1669-0.6581-0.00970.1594-0.09630.4049-0.08330.0876-0.04510.4102-0.07430.01240.5072-0.02040.4095-19.11260.993922.0063
53.75230.2357-0.03712.5129-1.06783.27920.18470.0562-0.22650.0748-0.1670.3092-0.01880.04920.01360.48010.0376-0.18240.3596-0.03550.8543-36.5393-19.88374.6704
61.5115-1.6357-0.5934.0792-0.04852.51580.1139-0.0494-0.33630.1904-0.0382-0.31810.10950.2291-0.06560.4236-0.009-0.17290.38580.01950.8349-33.0712-29.75796.6521
73.83030.0358-1.03052.4938-0.17733.75460.0642-0.0757-0.52410.0009-0.1397-0.4604-0.38140.60910.03830.4415-0.046-0.12260.4009-0.03780.8652-32.4775-35.4824-0.1079
81.51230.1167-0.23744.0135-0.7492.54730.00780.3966-0.6296-0.60790.1315-0.44830.04640.0091-0.13810.5972-0.0129-0.1170.4496-0.11410.7757-34.272-33.376-13.1154
91.13070.38210.05712.82581.14861.5632-0.02260.0650.04-0.50480.0530.3489-0.19340.0566-0.00820.51920.0045-0.23170.38090.01720.8437-38.4381-16.8065-7.5131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 18 )A-1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 101 )A19 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 134 )A102 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 247 )A135 - 247
5X-RAY DIFFRACTION5chain 'B' and (resid -4 through 34 )B-4 - 34
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 86 )B35 - 86
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 116 )B87 - 116
8X-RAY DIFFRACTION8chain 'B' and (resid 117 through 193 )B117 - 193
9X-RAY DIFFRACTION9chain 'B' and (resid 194 through 247 )B194 - 247

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