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- PDB-4hgo: 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohyd... -

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Basic information

Entry
Database: PDB / ID: 4hgo
Title2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron in complex with transition state mimic
Componentsacylneuraminate cytidylyltransferase
KeywordsTransferase / Hydrolase / Rossmann Fold / Phosphohydroylase
Function / homology
Function and homology information


3-deoxy-D-glycero-D-galacto-nonulopyranosonate 9-phosphatase / hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
KdsC family / HAD-superfamily hydrolase,subfamily IIIA / haloacid dehalogenase-like hydrolase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
deamino-beta-neuraminic acid / oxido(dioxo)vanadium / 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid phosphatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDaughtry, K.D. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis.
Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: chem_comp / citation_author
Item: _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID
Revision 2.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acylneuraminate cytidylyltransferase
B: acylneuraminate cytidylyltransferase
C: acylneuraminate cytidylyltransferase
D: acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,47814
Polymers73,4484
Non-polymers1,02910
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-65 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.296, 106.324, 74.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-325-

HOH

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Components

#1: Protein
acylneuraminate cytidylyltransferase / 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase


Mass: 18362.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1713 / Plasmid: pET-3A-626 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8A712
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO3
#4: Sugar ChemComp-KDN / deamino-beta-neuraminic acid / beta-deaminoneuraminic acid / 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid / sialic acid / Sialic acid


Type: D-saccharide, beta linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9
IdentifierTypeProgram
DKdnpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-keto-3-deoxy-b-D-nonulopyranosic acidCOMMON NAMEGMML 1.0
b-D-KdnpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdnSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% polyethylene glycol 3350 and 100 mM magnesium formate. Crystal soaked with 20 mM NaVN4 and 50 mM KDN for 1 week. Crystal dragged through Paratone prior to flash cooling, pH 7.5, VAPOR ...Details: 19% polyethylene glycol 3350 and 100 mM magnesium formate. Crystal soaked with 20 mM NaVN4 and 50 mM KDN for 1 week. Crystal dragged through Paratone prior to flash cooling, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 24, 2008 / Details: Helios multi-layer optics
RadiationMonochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→28.5 Å / Num. all: 38011 / Num. obs: 38011 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23.37 Å2 / Rsym value: 0.076 / Net I/σ(I): 6.29
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.485 / % possible all: 99

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E8M

3e8m


Resolution: 2.1→28.482 Å / SU ML: 0.28 / σ(F): 1.46 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 2000 5.26 %
Rwork0.1914 --
obs0.1942 38004 99.45 %
all-38004 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 56 176 5364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085280
X-RAY DIFFRACTIONf_angle_d1.0427117
X-RAY DIFFRACTIONf_dihedral_angle_d14.8611931
X-RAY DIFFRACTIONf_chiral_restr0.071800
X-RAY DIFFRACTIONf_plane_restr0.003904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.34691390.27572516X-RAY DIFFRACTION99
2.1525-2.21070.30851400.25732510X-RAY DIFFRACTION99
2.2107-2.27570.2961410.2312538X-RAY DIFFRACTION99
2.2757-2.34920.31421400.2222524X-RAY DIFFRACTION99
2.3492-2.43310.28071410.20942536X-RAY DIFFRACTION100
2.4331-2.53040.26471420.21072551X-RAY DIFFRACTION99
2.5304-2.64550.29581420.20632557X-RAY DIFFRACTION100
2.6455-2.78490.27911410.21522539X-RAY DIFFRACTION99
2.7849-2.95920.29241430.21292575X-RAY DIFFRACTION100
2.9592-3.18740.22661430.19952571X-RAY DIFFRACTION100
3.1874-3.50770.2831440.18982594X-RAY DIFFRACTION100
3.5077-4.0140.21741430.16062581X-RAY DIFFRACTION99
4.014-5.05260.15561470.14042645X-RAY DIFFRACTION100
5.0526-28.48460.20721540.17032767X-RAY DIFFRACTION100

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