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- PDB-6e85: 1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-... -

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Basic information

Entry
Database: PDB / ID: 6.0E+85
Title1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-4-phosphate Dehydrogenase from Klebsiella pneumoniae.
ComponentsD-threonate 4-phosphate dehydrogenase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 4-hydroxythreonine-4-phosphate Dehydrogenase
Function / homology
Function and homology information


NAD binding / oxidoreductase activity / metal ion binding
Similarity search - Function
PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / PYROPHOSPHATE 2- / 4-hydroxythreonine-4-phosphate dehydrogenase PdxA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.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.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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-threonate 4-phosphate dehydrogenase
B: D-threonate 4-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,65312
Polymers70,8482
Non-polymers80510
Water17,186954
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-90 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.355, 76.216, 92.113
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

POP

21A-964-

HOH

31B-910-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-threonate 4-phosphate dehydrogenase


Mass: 35423.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: pdxA, AN676_0302560, C4Z09_19135, C4Z14_08130, C4Z36_17000, C5Y00_08690, C5Y06_22400, CLQ72_17060, CVG30_05510
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) Magic
References: UniProt: A0A1Y0PY16, 4-hydroxythreonine-4-phosphate dehydrogenase

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Non-polymers , 6 types, 964 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 6.9 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 177342 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Rsym value: 0.053 / Χ2: 1 / Net I/σ(I): 24.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8637 / CC1/2: 0.8 / Rpim(I) all: 0.349 / Rrim(I) all: 0.654 / Rsym value: 0.549 / Χ2: 0.999 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HI1

2hi1


Resolution: 1.25→29.67 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.22 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1392 8941 5 %RANDOM
Rwork0.11384 ---
obs0.11509 168266 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.01 Å2
2--0.24 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.25→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 38 954 5915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0145678
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175167
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.6637810
X-RAY DIFFRACTIONr_angle_other_deg0.4891.62512145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35921.208265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27515915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4751542
X-RAY DIFFRACTIONr_chiral_restr0.0710.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.026700
X-RAY DIFFRACTIONr_gen_planes_other0.040.021004
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_it1.2610.9862955
X-RAY DIFFRACTIONr_mcbond_other1.2610.9862956
X-RAY DIFFRACTIONr_mcangle_it1.4581.4843783
X-RAY DIFFRACTIONr_mcangle_other1.4571.4853784
X-RAY DIFFRACTIONr_scbond_it1.6851.2682723
X-RAY DIFFRACTIONr_scbond_other1.6131.2472689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9811.793985
X-RAY DIFFRACTIONr_long_range_B_refined3.05714.8186603
X-RAY DIFFRACTIONr_long_range_B_other2.54513.46291
X-RAY DIFFRACTIONr_rigid_bond_restr8.784310845
X-RAY DIFFRACTIONr_sphericity_free19.8995693
X-RAY DIFFRACTIONr_sphericity_bonded6.937511096
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 646 -
Rwork0.225 12159 -
obs--97.68 %
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)
10.51260.1181-0.25290.7572-0.22311.3611-0.0316-0.0264-0.0785-0.032-0.0345-0.07340.09760.08970.06620.01620.0130.01080.01070.00920.01758.35883.304270.4178
20.6164-0.2478-0.56950.61790.18820.78550.05410.0907-0.0240.0357-0.0830.0761-0.0611-0.11920.02890.0121-0.00170.0060.099-0.03540.01893.2314-2.629539.5349
31.05570.2840.00830.5071-0.23511.0762-0.04880.0596-0.0335-0.1252-0.0246-0.08340.07850.04930.07350.03620.01210.02510.0279-0.0090.037511.40865.11160.1026
40.3305-0.0286-0.07050.9898-0.67491.61430.0082-0.0099-0.00170.09380.04010.1009-0.0825-0.1551-0.04830.01820.01010.01150.01950.00290.011222.28883.94983.6009
50.6203-0.1188-0.27830.41710.15350.83080.0241-0.03310.0248-0.0174-0.0267-0.0193-0.05440.04370.00260.006-0.0119-0.00060.05110.0040.002626.8473-5.734533.4301
61.6957-0.61260.82741.306-0.62022.1367-0.0582-0.16080.03680.30680.09150.0845-0.2847-0.3009-0.03340.11680.05040.04950.08120.01610.033819.32076.365713.8578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 146
2X-RAY DIFFRACTION2A147 - 288
3X-RAY DIFFRACTION3A289 - 328
4X-RAY DIFFRACTION4B2 - 146
5X-RAY DIFFRACTION5B147 - 289
6X-RAY DIFFRACTION6B290 - 327

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