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- PDB-8u9e: Crystal Structure of Staphylococcus aureus Pdx1 -

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Basic information

Entry
Database: PDB / ID: 8u9e
TitleCrystal Structure of Staphylococcus aureus Pdx1
ComponentsPyridoxal 5'-phosphate synthase subunit PdxS
KeywordsBIOSYNTHETIC PROTEIN / Synthase / Vitamin B6 synthase
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine metabolic process / glycosyltransferase activity
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsBarra, A.L.C. / Nascimento, A.S.
Funding support Brazil, Germany, 9items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26722-8 Brazil
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
Sao Paulo Research Foundation (FAPESP)2020/03983-9 Brazil
Sao Paulo Research Foundation (FAPESP)2019/26428-3 Brazil
Sao Paulo Research Foundation (FAPESP)2019/20219-3 Brazil
Sao Paulo Research Foundation (FAPESP)2019/00899-0 Brazil
Sao Paulo Research Foundation (FAPESP)2018/21213-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)302992/2021-9 Brazil
German Research Foundation (DFG)390715994 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface.
Authors: Barra, A.L.C. / Ullah, N. / Brognaro, H. / Gutierrez, R.F. / Wrenger, C. / Betzel, C. / Nascimento, A.S.
History
DepositionSep 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,09912
Polymers64,3182
Non-polymers78110
Water181
1
A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)390,59272
Polymers385,90612
Non-polymers4,68560
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area49680 Å2
ΔGint-190 kcal/mol
Surface area99630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.407, 182.407, 96.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyridoxal 5'-phosphate synthase subunit PdxS


Mass: 32158.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pdxS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1HGG1

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Non-polymers , 5 types, 11 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris base; BICINE, pH 8.5; 1.6% w/v dipeptides mix, 20% v/v glycerol; 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.959→82.234 Å / Num. obs: 12897 / % possible obs: 100 % / Redundancy: 30 % / Biso Wilson estimate: 92.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.029 / Net I/σ(I): 17.1
Reflection shellResolution: 2.959→3.01 Å / Redundancy: 33.2 % / Rmerge(I) obs: 2.058 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 640 / CC1/2: 0.76 / Rpim(I) all: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→82.2 Å / SU ML: 0.5232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 562 4.6 %
Rwork0.2236 11650 -
obs0.2255 12212 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.58 Å2
Refinement stepCycle: LAST / Resolution: 3.02→82.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 46 1 3457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00133502
X-RAY DIFFRACTIONf_angle_d0.38714751
X-RAY DIFFRACTIONf_chiral_restr0.0385550
X-RAY DIFFRACTIONf_plane_restr0.0034644
X-RAY DIFFRACTIONf_dihedral_angle_d3.7771540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.320.37571370.30472898X-RAY DIFFRACTION100
3.32-3.80.29731500.24862857X-RAY DIFFRACTION100
3.81-4.790.26331260.20862929X-RAY DIFFRACTION100
4.79-82.20.23411490.20782966X-RAY DIFFRACTION99.94
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)
18.09194210922-0.2180684695841.116974955946.3483443576-0.962701348920.2931304125660.104044200751-1.702970474080.5240205851010.413796119263-0.2466302950910.313064985235-1.13550187299-0.1092124873480.5550756200841.4832964443-0.07409643192590.329374036310.801425442158-0.4298956374130.855016940974-12.262245416341.589128202334.0470329584
21.178117457310.5968208404050.7250104270717.848144173762.693519436591.165320348880.354710919943-1.19092677630.697607101771.829436682670.002409238712390.16584668504-0.877808287252-0.36285622428-0.1026738717121.495412932090.1455491980330.3839903053680.935463768599-0.236170616240.964254388951-20.924295848833.295421757434.0335426479
34.578743919570.007492560811382.090267147662.0830054242-0.7826856698393.958161029090.4118758346-0.5476876086550.309662623073-0.43679495962-0.1788278539890.0656360223901-1.22008691223-0.236048781144-0.280273010481.04805747610.2232705401370.248802992130.811452791769-0.1861013532010.796397926644-23.861317917829.787430675121.6837194805
44.870667278870.8186077447662.812495733352.233077253860.4089042060412.28057669181-0.0815118758048-0.5220207732390.1520139323590.1634512407490.2141848783840.113077296271-0.65621512433-0.349452145388-0.159712004381.181759689030.1123437900850.2819136803620.628121078311-0.1358583406360.680021403919-10.642818360834.307958869214.1226188034
52.52587302949-1.198513217820.952507385393.71024617943-0.3772541731750.5565550464660.1020372928080.06077626300680.679980040553-0.01329241944460.01749974750340.116198244764-0.704441459954-0.06909623444050.01074784074921.03685364123-0.001417005705610.2741264534120.630794560689-0.01930551111240.751869804504-7.7268892746938.35738060558.39724192491
63.379891894361.47886239816-3.052408597933.11249161271-1.357974718783.839680637410.89345244232-0.695374615499-0.01177326644230.885719183721-0.1885639657880.836172490121-0.1429112116280.921211687007-0.583270536061.69498349145-0.06962701578670.3886553539610.663767437607-0.2230317219861.01526199126-4.5943663322237.83539815630.4313936248
70.5089505926220.0995200204307-0.2224725678970.6658239948830.1309218281730.4929182691080.184379488865-0.3975870284850.6041523957170.08403457487250.110999450089-0.062218101358-0.02685629542110.2098394062370.05595939272091.9467425756-0.2522998935370.4659029785620.900741208705-0.5388053668561.114115592533.4486372171145.184904953432.0881774951
87.25438767116-0.8413749732912.5916723665.698918272742.143368438152.49715616872-0.358472393926-0.8592845188720.4789753260280.9945521071580.331575059076-0.155230551158-0.6927021027930.9111198512450.08741727422871.21152802712-0.238218945833-0.02214458351651.07759448964-0.2653658533750.63579314531123.943929070533.231075022834.1834806947
93.87788985592-0.07143404911210.09963057165072.29805870436-0.06051855714381.222270002480.0797157500012-0.01191466581750.287460753510.2922468095340.163042521416-0.246526749954-0.6245743484480.489841602672-0.1974347914310.878266773365-0.229128361935-0.003809985633230.668799609507-0.2134392080380.64530306883420.458538431529.831776791717.1348447009
100.169564547226-0.3088584825080.9425084475390.779289839886-2.309618206246.937339419040.0604824365571-0.1682665448680.230055869539-0.09818988539810.13319167539-0.452477586627-0.7538393011121.38777230028-0.2372910591770.813251554917-0.2929863942680.2217383808630.973423000721-0.08424783294460.81878329804125.517471163425.4661868851-5.24679104939
112.51314050656-1.078240089322.940739586281.79412720704-0.471514617583.81198533318-0.0533137147231-0.5724719156770.4961757540430.6959258326050.413700688382-0.649347955387-0.2598512925770.390267786297-0.0445700197860.971490347881-0.146540551491-0.2080418698081.20728369152-0.4149090403080.82372220499234.317663072623.529034472322.7563971466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 45 )AA17 - 451 - 29
22chain 'A' and (resid 46 through 83 )AA46 - 8330 - 60
33chain 'A' and (resid 84 through 118 )AA84 - 11861 - 95
44chain 'A' and (resid 119 through 177 )AA119 - 17796 - 154
55chain 'A' and (resid 178 through 227 )AA178 - 227155 - 204
66chain 'A' and (resid 228 through 244 )AA228 - 244205 - 221
77chain 'A' and (resid 245 through 272 )AA245 - 272222 - 249
88chain 'B' and (resid 17 through 83 )BD17 - 831 - 60
99chain 'B' and (resid 84 through 177 )BD84 - 17761 - 154
1010chain 'B' and (resid 178 through 190 )BD178 - 190155 - 167
1111chain 'B' and (resid 191 through 272 )BD191 - 272168 - 249

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