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- PDB-1yxo: Crystal Structure of pyridoxal phosphate biosynthetic protein Pdx... -

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Basic information

Entry
Database: PDB / ID: 1yxo
TitleCrystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593
Components4-hydroxythreonine-4-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / PA0593 / PYRIDOXINE BIOSYNTHESIS / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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 / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / 4-hydroxythreonine-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsLiu, Y. / Xu, X. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593
Authors: Liu, Y. / Xu, X. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 4-hydroxythreonine-4-phosphate dehydrogenase 1
B: 4-hydroxythreonine-4-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00514
Polymers70,4952
Non-polymers50912
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint5 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.259, 59.307, 199.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35247.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pdxA1 / Plasmid: pEt15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I5U4, 4-hydroxythreonine-4-phosphate dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.98046
SYNCHROTRONAPS 14-BM-D20.98032
SYNCHROTRONAPS 14-BM-D30.9648
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980461
20.980321
30.96481
ReflectionResolution: 2.01→80 Å / Num. all: 43764 / Num. obs: 42938 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 8.5
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.05 / Num. unique all: 4188 / Rsym value: 0.201 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 2.01→36.68 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 410646.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: O v8.0 was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1292 3 %RANDOM
Rwork0.198 ---
obs0.198 42938 98.1 %-
all-43764 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1599 Å2 / ksol: 0.340458 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2--7.27 Å20 Å2
3----3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.01→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 32 450 5392
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.01→2.14 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 190 2.8 %
Rwork0.23 6569 -
obs-6759 94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EOH_XPLOR_PAR.TXTEOH_XPLOR_TOP.TXT
X-RAY DIFFRACTION5MSE_PAR.TXTMSE_TOP.TXT

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