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- PDB-1znn: Structure of the synthase subunit of PLP synthase -

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Basic information

Entry
Database: PDB / ID: 1znn
TitleStructure of the synthase subunit of PLP synthase
ComponentsPLP SYNTHASE
KeywordsBIOSYNTHETIC PROTEIN / TIM BARREL
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / amino acid metabolic process
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhu, J. / Burgner, J.W. / Harms, E. / Belitsky, B.R. / Smith, J.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A New Arrangement of (beta/alpha)8 Barrels in the Synthase Subunit of PLP Synthase.
Authors: Zhu, J. / Burgner, J.W. / Harms, E. / Belitsky, B.R. / Smith, J.L.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLP SYNTHASE
B: PLP SYNTHASE
C: PLP SYNTHASE
D: PLP SYNTHASE
E: PLP SYNTHASE
F: PLP SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,01324
Polymers210,1516
Non-polymers1,86218
Water27,1491507
1
A: PLP SYNTHASE
B: PLP SYNTHASE
C: PLP SYNTHASE
D: PLP SYNTHASE
E: PLP SYNTHASE
F: PLP SYNTHASE
hetero molecules

A: PLP SYNTHASE
B: PLP SYNTHASE
C: PLP SYNTHASE
D: PLP SYNTHASE
E: PLP SYNTHASE
F: PLP SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,02648
Polymers420,30212
Non-polymers3,72436
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area48510 Å2
ΔGint-536 kcal/mol
Surface area97820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)162.531, 163.917, 186.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2889-

HOH

21A-3216-

HOH

31A-3218-

HOH

41B-2890-

HOH

51D-2954-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 20 - 271 / Label seq-ID: 51 - 302

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
PLP SYNTHASE


Mass: 35025.188 Da / Num. of mol.: 6 / Fragment: SYNTHASE SUBUNIT / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: Q5L3Y2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1507 / 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: 3.1 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG 8000, (NH4)2SO4, cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 17, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 125880 / Num. obs: 125880 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.618 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19804 6320 5 %RANDOM
Rwork0.15925 ---
all0.198 125880 --
obs0.16117 119560 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.97 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11034 0 108 1507 12649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211268
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.97915228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04751458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37824.051474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.465151950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391590
X-RAY DIFFRACTIONr_chiral_restr0.110.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028334
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.46172
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.57836
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.552006
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.4150
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.55167
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.57468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.431211610
X-RAY DIFFRACTIONr_scbond_it2.58734162
X-RAY DIFFRACTIONr_scangle_it4.114.53618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1826 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.211
2Bmedium positional0.351
3Cmedium positional0.221
4Dmedium positional0.281
5Emedium positional0.331
6Fmedium positional0.251
1Amedium thermal2.615
2Bmedium thermal3.065
3Cmedium thermal2.755
4Dmedium thermal2.915
5Emedium thermal4.65
6Fmedium thermal1.995
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 475 -
Rwork0.215 8760 -
obs--99.83 %
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)
11.8137-0.1281-0.0761.1229-0.69591.608-0.0263-0.17290.01750.16070.02180.1573-0.0449-0.34170.0045-0.3502-0.04360.0058-0.1838-0.0035-0.25784.78238.18620.77
21.59280.53020.25111.4946-0.23020.69140.0053-0.00540.20620.075-0.0060.1377-0.1298-0.06010.0007-0.29340.00040.0035-0.39940.0171-0.245732.38962.8559.124
31.3228-0.01570.99181.1284-0.03922.7133-0.0862-0.35680.42730.1918-0.00020.0281-0.5611-0.0380.0865-0.0217-0.0783-0.0054-0.243-0.1731-0.046353.55782.1134.992
40.70690.5826-0.42131.1709-0.64412.37330.1741-0.36640.41730.3593-0.11650.1999-0.5575-0.1309-0.05760.1096-0.06390.05490.3535-0.30360.079246.90776.39872.605
51.4378-0.5942-0.58230.2830.21311.21460.1436-0.4762-0.1947-0.02990.02550.303-0.1597-0.017-0.1691-0.0694-0.0395-0.00460.5994-0.06150.082719.67551.24484.262
61.27410.1345-0.0840.5990.45852.6949-0.0367-0.36390.06620.1821-0.02160.1237-0.0728-0.49240.0584-0.2059-0.06560.08510.37290.0722-0.1139-1.58132.09858.38
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 27149 - 302
2X-RAY DIFFRACTION2BB18 - 27149 - 302
3X-RAY DIFFRACTION3CC18 - 27149 - 302
4X-RAY DIFFRACTION4DD18 - 27149 - 302
5X-RAY DIFFRACTION5EE18 - 27149 - 302
6X-RAY DIFFRACTION6FF18 - 27149 - 302

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