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- PDB-2nv1: Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase fro... -

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Basic information

Entry
Database: PDB / ID: 2nv1
TitleStructure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis
ComponentsPyridoxal biosynthesis lyase pdxS
KeywordsLYASE / (beta/alpha)8-barrel / Synthase
Function / homology
Function and homology information


amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / amino acid metabolic process / identical protein binding
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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsStrohmeier, M. / Tews, I. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of a bacterial pyridoxal 5'-phosphate synthase complex
Authors: Strohmeier, M. / Raschle, T. / Mazurkiewicz, J. / Rippe, K. / Sinning, I. / Fitzpatrick, T.B. / Tews, I.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
E: Pyridoxal biosynthesis lyase pdxS
F: Pyridoxal biosynthesis lyase pdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,46041
Polymers198,0606
Non-polymers1,40035
Water42,6422367
1
A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
E: Pyridoxal biosynthesis lyase pdxS
F: Pyridoxal biosynthesis lyase pdxS
hetero molecules

A: Pyridoxal biosynthesis lyase pdxS
B: Pyridoxal biosynthesis lyase pdxS
C: Pyridoxal biosynthesis lyase pdxS
D: Pyridoxal biosynthesis lyase pdxS
E: Pyridoxal biosynthesis lyase pdxS
F: Pyridoxal biosynthesis lyase pdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,92082
Polymers396,12112
Non-polymers2,80070
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area46730 Å2
ΔGint-522 kcal/mol
Surface area101790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.055, 106.202, 182.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-4014-

HOH

21A-4334-

HOH

31D-4049-

HOH

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Components

#1: Protein
Pyridoxal biosynthesis lyase pdxS / Superoxide-inducible protein 7 / SOI7


Mass: 33010.047 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: strain 168 / Plasmid: pET21a, pET-BsPdx1-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3] / References: UniProt: P37527, Lyases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2367 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 15-20% ethanol, 200mM MgCl2, 100mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2005 / Details: ESRF
RadiationMonochromator: ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 118303 / Num. obs: 116594 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.103 / Net I/σ(I): 9
Reflection shellResolution: 2.08→2.1 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.479 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNN

1znn


Resolution: 2.08→48.68 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.867 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19139 5782 5 %RANDOM
Rwork0.14163 ---
obs0.14414 110798 98.59 %-
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: 28.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 2.08→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11340 0 68 2367 13775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211631
X-RAY DIFFRACTIONr_bond_other_d0.0030.027756
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.98915753
X-RAY DIFFRACTIONr_angle_other_deg0.976319055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04351519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49625.309469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.798152068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7511565
X-RAY DIFFRACTIONr_chiral_restr0.090.21821
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022078
X-RAY DIFFRACTIONr_nbd_refined0.2320.22966
X-RAY DIFFRACTIONr_nbd_other0.2120.29116
X-RAY DIFFRACTIONr_nbtor_refined0.1730.25736
X-RAY DIFFRACTIONr_nbtor_other0.0880.26073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0860.25
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.2223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.2117
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.031.57783
X-RAY DIFFRACTIONr_mcbond_other0.2141.53127
X-RAY DIFFRACTIONr_mcangle_it1.603212090
X-RAY DIFFRACTIONr_scbond_it2.61634248
X-RAY DIFFRACTIONr_scangle_it3.9724.53626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 413 -
Rwork0.179 8145 -
obs--99.17 %
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)
10.0139-0.0301-0.04480.62050.02590.1540.01450.0020.00770.1178-0.00330.10890.0084-0.0233-0.01120.0036-0.00510.0503-0.03380.0014-0.00229.509244.27683.8387
20.0702-0.00080.00660.26730.14190.3451-0.01040.0077-0.00120.0445-0.02330.04420.0597-0.06010.0338-0.0096-0.03650.0275-0.0093-0.0101-0.019430.798915.415357.8706
30.0025-0.00720.02740.3616-0.18080.47770.0164-0.0269-0.0082-0.07160.00350.0690.0741-0.0699-0.0199-0.0167-0.034-0.0301-0.006-0.0121-0.014730.301423.226919.8049
40.0483-0.04390.03860.47260.0050.20910.02960.0161-0.0188-0.0916-0.02820.0741-0.0138-0.0421-0.0014-0.01890.0092-0.048-0.0066-0.0057-0.013228.681460.09257.4672
50.0123-0.0282-0.06390.29050.13260.33270.01440.01790.0047-0.0201-0.04410.0606-0.0551-0.04260.0297-0.01920.0218-0.0203-0.0049-0.0077-0.009627.516488.930533.0999
60.0418-0.1150.03220.3394-0.17950.3848-0.01280.00990.00060.06660.03420.0553-0.0568-0.0574-0.0213-0.00660.01830.0297-0.02060.0054-0.014927.569980.659771.3547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 2719 - 274
2X-RAY DIFFRACTION2BB10 - 27013 - 273
3X-RAY DIFFRACTION3CC7 - 27110 - 274
4X-RAY DIFFRACTION4DD8 - 27211 - 275
5X-RAY DIFFRACTION5EE6 - 2709 - 273
6X-RAY DIFFRACTION6FF12 - 27115 - 274

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