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- PDB-4hgn: Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate PHOSP... -

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Basic information

Entry
Database: PDB / ID: 4hgn
TitleCrystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate PHOSPHOHYDROLASE from Bacteroides thetaiotaomicron
Components2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
KeywordsHYDROLASE / Rossmann Fold / Phosphohydroylase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
KdsC family / 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
FORMIC ACID / Putative hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
B: 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
C: 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
D: 2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47810
Polymers77,2894
Non-polymers1896
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-66 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.522, 91.198, 170.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-keto-3-deoxy-D-manno-octulosonate 8-phosphate phosphohydrolase


Mass: 19322.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1677 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8A748, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 1.88 Å3/Da / Density % sol: 34.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes, 30% polyethylene glycol MME 550, 40 mM magnesium chloride. Crystal dragged through Paratone prior to flash cooling, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→36.64 Å / Num. all: 50327 / Num. obs: 50327 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 20.25 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.79 / Num. unique all: 4618 / Rsym value: 0.432 / % possible all: 79.7

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Processing

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

3e8m


Resolution: 1.8→36.64 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2300 5.06 %Random
Rwork0.1756 ---
all0.1777 45439 --
obs-45439 82.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 10 329 5403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085184
X-RAY DIFFRACTIONf_angle_d1.0947024
X-RAY DIFFRACTIONf_dihedral_angle_d12.9491932
X-RAY DIFFRACTIONf_chiral_restr0.077779
X-RAY DIFFRACTIONf_plane_restr0.005895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83920.25451060.19812010X-RAY DIFFRACTION63
1.8392-1.88190.27531030.21182089X-RAY DIFFRACTION64
1.8819-1.9290.25121100.2052160X-RAY DIFFRACTION67
1.929-1.98120.27981180.19952160X-RAY DIFFRACTION66
1.9812-2.03950.22911330.19462239X-RAY DIFFRACTION71
2.0395-2.10530.23181260.18122368X-RAY DIFFRACTION73
2.1053-2.18050.25531480.17242447X-RAY DIFFRACTION76
2.1805-2.26780.23511660.17252558X-RAY DIFFRACTION80
2.2678-2.3710.25321400.17572709X-RAY DIFFRACTION83
2.371-2.4960.20581510.17852897X-RAY DIFFRACTION89
2.496-2.65230.21871620.19492997X-RAY DIFFRACTION92
2.6523-2.8570.23621520.19443107X-RAY DIFFRACTION94
2.857-3.14440.22421610.19313221X-RAY DIFFRACTION97
3.1444-3.59910.21061670.17563265X-RAY DIFFRACTION99
3.5991-4.53310.19251700.14513382X-RAY DIFFRACTION100
4.5331-36.640.18991870.16593530X-RAY DIFFRACTION100

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