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- PDB-3tsn: 4-hydroxythreonine-4-phosphate dehydrogenase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 3tsn
Title4-hydroxythreonine-4-phosphate dehydrogenase from Campylobacter jejuni
Components4-hydroxythreonine-4-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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, epsilonproteobacteria / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Unknown ligand / 4-hydroxythreonine-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsOsipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 4-hydroxythreonine-4-phosphate dehydrogenase from Campylobacter jejuni.
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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_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_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_asym_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.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_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: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
C: 4-hydroxythreonine-4-phosphate dehydrogenase
D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,26712
Polymers168,0324
Non-polymers2358
Water3,045169
1
A: 4-hydroxythreonine-4-phosphate dehydrogenase
B: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1346
Polymers84,0162
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-47 kcal/mol
Surface area33120 Å2
MethodPISA
2
C: 4-hydroxythreonine-4-phosphate dehydrogenase
D: 4-hydroxythreonine-4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1346
Polymers84,0162
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-47 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.938, 141.938, 121.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 42008.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1239, pdxA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PN58, 4-hydroxythreonine-4-phosphate dehydrogenase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M DL-malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2011
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.63→46.4 Å / Num. all: 71267 / Num. obs: 71267 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 67.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.12 / Num. unique all: 3531 / Rsym value: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.63→46.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.564 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24059 3599 5.1 %RANDOM
Rwork0.18936 ---
obs0.19197 67575 99.87 %-
all-67575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.099 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2--1.72 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.63→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11708 0 83 169 11960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.96916169
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12824.65514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.919152302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3231517
X-RAY DIFFRACTIONr_chiral_restr0.0960.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7781.57256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.509211616
X-RAY DIFFRACTIONr_scbond_it2.25134786
X-RAY DIFFRACTIONr_scangle_it3.7834.54545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 282 -
Rwork0.288 4944 -
obs-5226 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)
10.96890.10290.24591.03040.5912.5227-0.00570.0502-0.1321-0.03450.05170.0220.20140.0414-0.0460.0495-0.026-0.04110.02820.03060.074549.087343.667968.915
22.11510.3401-1.39511.068-0.3912.5013-0.047-0.583-0.34370.2506-0.1001-0.06460.32930.43550.14710.20580.0624-0.06350.25920.11920.148874.83836.7332100.2705
30.91980.1502-0.27561.4255-1.15243.4604-0.09210.0012-0.0613-0.245-0.1-0.19990.00910.40550.19210.1052-0.0638-0.01970.11970.0780.174428.260718.80964.8092
41.29520.46451.08560.80140.88012.1908-0.0535-0.32570.1359-0.0124-0.13060.1375-0.2779-0.16160.18410.1339-0.029-0.09620.113-0.01240.15566.060734.459936.1015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 363
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A601
4X-RAY DIFFRACTION2B0 - 363
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B601
7X-RAY DIFFRACTION3C0 - 363
8X-RAY DIFFRACTION3C501
9X-RAY DIFFRACTION3C601
10X-RAY DIFFRACTION4D0 - 363
11X-RAY DIFFRACTION4D501
12X-RAY DIFFRACTION4D601

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