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- PDB-3e8m: Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto... -

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Basic information

Entry
Database: PDB / ID: 3e8m
TitleStructure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily
ComponentsAcylneuraminate cytidylyltransferase
KeywordsTRANSFERASE / 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase / Nucleotidyltransferase
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 / 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
ACETIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid phosphatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsLu, Z. / Wang, L. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-Function Analysis of 2-Keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members.
Authors: Lu, Z. / Wang, L. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53536
Polymers73,4484
Non-polymers2,08632
Water19,5821087
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-91 kcal/mol
Surface area26430 Å2
MethodPISA
2
A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
hetero molecules

A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,06972
Polymers146,8978
Non-polymers4,17364
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area31120 Å2
ΔGint-199 kcal/mol
Surface area47480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.243, 107.482, 75.093
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
11B-264-

HOH

21B-350-

HOH

31C-326-

HOH

41D-301-

HOH

51D-426-

HOH

61D-477-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acylneuraminate cytidylyltransferase


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

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Non-polymers , 8 types, 1119 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1087 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% w/v polyethelene glycol (PEG) 4,000, 0.1 M Tris HCl pH 8.5, 0.2 M sodium acetate and 10 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 258326 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.047 / Χ2: 0.997 / Net I/σ(I): 43.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / Num. unique all: 22333 / Χ2: 1.011 / % possible all: 84.8

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
MOLREPphasing
DENZOdata reduction
RefinementStarting model: pdb entry 1K1E

1k1e


Resolution: 1.1→28.782 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.09 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.141 24703 5.05 %RANDOM
Rwork0.127 ---
obs0.128 257759 94.97 %-
all-257889 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.109 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 102.45 Å2 / Biso mean: 17.685 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.077 Å2-0 Å2-0 Å2
2---1.633 Å2-0 Å2
3----0.953 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.1→28.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10811 0 171 1197 12179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d0.031
X-RAY DIFFRACTIONf_similar_dist0
X-RAY DIFFRACTIONf_from_restr_planes0.026
X-RAY DIFFRACTIONf_zero_chiral_vol0.073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.1-1.16930.173434370.1562X-RAY DIFFRACTION6674381.6
1.1693-1.25960.13940650.1191X-RAY DIFFRACTION7691494.2
1.2596-1.38630.12442910.1049X-RAY DIFFRACTION7862996.6
1.3863-1.58690.122342920.0962X-RAY DIFFRACTION8011998
1.5869-1.99930.125743960.1029X-RAY DIFFRACTION8093899.4
1.9993-28.79230.137142220.1244X-RAY DIFFRACTION81464100

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