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- PDB-4hgq: Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-ga... -

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Basic information

Entry
Database: PDB / ID: 4hgq
TitleCrystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron
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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 2.28 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 1.3Feb 10, 2021Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_conn_angle ...citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._citation_author.identifier_ORCID / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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

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Assembly

Deposited unit
A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
E: Acylneuraminate cytidylyltransferase
F: Acylneuraminate cytidylyltransferase
G: Acylneuraminate cytidylyltransferase
H: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,62716
Polymers146,4328
Non-polymers1948
Water10,124562
1
A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3138
Polymers73,2164
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-70 kcal/mol
Surface area25620 Å2
MethodPISA
2
E: Acylneuraminate cytidylyltransferase
F: Acylneuraminate cytidylyltransferase
G: Acylneuraminate cytidylyltransferase
H: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3138
Polymers73,2164
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-68 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.941, 94.116, 161.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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


Mass: 18304.027 Da / Num. of mol.: 8 / Mutation: E56A
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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM magnesium chloride, 23% polyethylene glycol 3350. The crystal was dragged through paratone prior to flash-cooling, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 28, 2009 / 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: 2.28→37.1 Å / Num. all: 62511 / Num. obs: 62511 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.21 % / Rsym value: 0.0878 / Net I/σ(I): 11.6
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 4.63 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3877 / Rsym value: 0.4648 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3e8m

3e8m


Resolution: 2.28→37.1 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 3557 3.19 %random
Rwork0.1954 ---
obs0.1971 62511 93.24 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.641 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1--3.193 Å20 Å20 Å2
2---0.2331 Å2-0 Å2
3---3.4261 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.28→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10320 0 8 562 10890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710527
X-RAY DIFFRACTIONf_angle_d1.01514199
X-RAY DIFFRACTIONf_dihedral_angle_d15.393881
X-RAY DIFFRACTIONf_chiral_restr0.071587
X-RAY DIFFRACTIONf_plane_restr0.0031822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.36150.32553210.27879774X-RAY DIFFRACTION85
2.3615-2.4560.32743230.2610080X-RAY DIFFRACTION87
2.456-2.56780.32133320.25110367X-RAY DIFFRACTION90
2.5678-2.70310.29783690.224810639X-RAY DIFFRACTION92
2.7031-2.87240.30093320.224210907X-RAY DIFFRACTION94
2.8724-3.09410.26913690.217110909X-RAY DIFFRACTION95
3.0941-3.40520.26423740.202811140X-RAY DIFFRACTION96
3.4052-3.89750.24013820.176311205X-RAY DIFFRACTION97
3.8975-4.90870.17893700.138211329X-RAY DIFFRACTION98
4.9087-37.10.18773850.157911452X-RAY DIFFRACTION99

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