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- PDB-6xmy: Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 6xmy
TitleCrystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / 4-hydroxythreonine-4-phosphate dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / cobalt ion binding / NAD binding / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
4-hydroxythreonine-4-phosphate dehydrogenase / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / 4-hydroxythreonine-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD
Authors: DeBouver, N.D. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,10111
Polymers35,7751
Non-polymers1,32610
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.350, 36.770, 56.620
Angle α, β, γ (deg.)90.000, 103.070, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxythreonine-4-phosphate dehydrogenase / 4-(phosphohydroxy)-L-threonine dehydrogenase


Mass: 35774.523 Da / Num. of mol.: 1 / Fragment: LepnA.00116.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: pdxA, lpg0299 / Plasmid: LepnA.00116.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q3V872, 4-hydroxythreonine-4-phosphate dehydrogenase

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Non-polymers , 6 types, 414 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: LepnA.00116.a.B1.PS38420 [Barcode: 314605h9, PuckID: gpx5-5, Cryo: 15% EG, Concentration: 14.95 mg/mL] 100 mM Bis-Tris/ Hydrochloric acid pH 5.5, 200 mM Lithium sulfate, 25% (w/v) PEG 3350

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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 MX-300 / Detector: CCD / Date: Feb 13, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 59918 / % possible obs: 98.1 % / Redundancy: 4.051 % / Biso Wilson estimate: 19.509 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.099 / Χ2: 1 / Net I/σ(I): 13.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.443.4030.4993.0441660.8420.59292.6
1.44-1.484.0030.497442520.8920.57597.3
1.48-1.524.1360.4625.1641490.910.53297.6
1.52-1.574.1310.426.1440320.9310.48598.1
1.57-1.624.1590.3787.1739360.9320.43698.2
1.62-1.674.1380.3078.4738520.950.35498.8
1.67-1.744.1610.2489.9336900.9740.28698.7
1.74-1.814.150.20511.4235490.9790.23798.9
1.81-1.894.1290.16413.2734360.9850.18999.2
1.89-1.984.1580.12715.2232820.9890.14799.2
1.98-2.094.1310.09817.2431180.9930.11499.2
2.09-2.214.1310.08218.8229660.9930.09599.1
2.21-2.374.1020.07120.4427840.9940.08298.9
2.37-2.564.0880.06421.7526080.9950.07499.2
2.56-2.84.070.05923.1224140.9950.06999.1
2.8-3.134.0580.05524.5421500.9950.06398.7
3.13-3.614.0360.04826.1619220.9950.05698.1
3.61-4.433.9730.04627.3616100.9960.05397.8
4.43-6.263.9140.04727.4712810.9960.05497.9
6.26-503.5480.04826.477210.9940.05796.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R8K

1r8k


Resolution: 1.4→40.23 Å / SU ML: 0.1328 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.0581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1717 1950 3.25 %
Rwork0.138 57959 -
obs0.1391 59909 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.78 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 80 404 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532687
X-RAY DIFFRACTIONf_angle_d0.90983689
X-RAY DIFFRACTIONf_chiral_restr0.0745439
X-RAY DIFFRACTIONf_plane_restr0.0058464
X-RAY DIFFRACTIONf_dihedral_angle_d15.8593990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.27861250.2283895X-RAY DIFFRACTION92.37
1.44-1.470.23791290.17714068X-RAY DIFFRACTION97.18
1.47-1.520.19111390.14354078X-RAY DIFFRACTION97.64
1.52-1.570.19351210.13434104X-RAY DIFFRACTION98.12
1.57-1.620.17871320.12734128X-RAY DIFFRACTION98.2
1.62-1.690.18981530.1274170X-RAY DIFFRACTION98.83
1.69-1.760.1761500.12614097X-RAY DIFFRACTION98.72
1.76-1.860.17061470.12934169X-RAY DIFFRACTION99.13
1.86-1.970.1871440.1284177X-RAY DIFFRACTION99.22
1.97-2.130.17221270.12934188X-RAY DIFFRACTION99.31
2.13-2.340.16071340.13284193X-RAY DIFFRACTION99.13
2.34-2.680.17161440.14194210X-RAY DIFFRACTION99.23
2.68-3.370.1671670.1414191X-RAY DIFFRACTION98.57
3.37-40.230.14541380.13744291X-RAY DIFFRACTION97.84

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