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- PDB-4z1c: Structure of Cadmium bound KDO8PS from H.pylori -

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Basic information

Entry
Database: PDB / ID: 4z1c
TitleStructure of Cadmium bound KDO8PS from H.pylori
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / Helicobacter pylori / lipopolysaccharide biosynthesis / metal bound
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsLee, B.J. / Cho, S. / Im, H. / Yoon, H.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).
Authors: Cho, S. / Im, H. / Lee, K.Y. / Chen, J. / Kang, H.J. / Yoon, H.J. / Min, K.H. / Lee, K.R. / Park, H.J. / Lee, B.J.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9894
Polymers60,7642
Non-polymers2252
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.353, 51.017, 78.667
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-dehydro-3-deoxyphosphooctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho-2-dehydro-3-deoxyoctonate aldolase


Mass: 30381.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: kdsA, HP_0003 / Plasmid: pCOLD I / Production host: Escherichia coli (E. coli)
References: UniProt: P56060, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 36113 / % possible obs: 92.2 % / Redundancy: 3.5 % / Net I/σ(I): 32.85

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.93→28.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.361 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21181 1915 5 %RANDOM
Rwork0.19063 ---
obs0.19174 36113 93.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.466 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å20.9 Å2
2---1.02 Å20 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.93→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 2 352 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194068
X-RAY DIFFRACTIONr_bond_other_d0.0010.024004
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9785492
X-RAY DIFFRACTIONr_angle_other_deg1.19939230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93525.057174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24715748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02876
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.27534068
X-RAY DIFFRACTIONr_sphericity_free29.1285104
X-RAY DIFFRACTIONr_sphericity_bonded10.86954261
LS refinement shellResolution: 1.93→1.98 Å
RfactorNum. reflection% reflection
Rfree0.354 138 -
Rwork0.328 2725 -
obs--96.11 %

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