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- PDB-4hgp: Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosp... -

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Basic information

Entry
Database: PDB / ID: 4hgp
TitleCrystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
KeywordsHYDROLASE / Rossmann Fold / Phosphohydroylase
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / : / HAD-superfamily hydrolase,subfamily IIIA / 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
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / oxido(dioxo)vanadium / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_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_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 1.4Feb 10, 2021Group: Database references / Structure summary / Category: chem_comp / citation_author
Item: _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID
Revision 1.5Sep 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: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8174
Polymers19,4551
Non-polymers3613
Water3,189177
1
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
hetero molecules

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
hetero molecules

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
hetero molecules

A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,26716
Polymers77,8214
Non-polymers1,44612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area12550 Å2
ΔGint-89 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.846, 79.846, 52.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-424-

HOH

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Components

#1: Protein 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC / KDO 8-P phosphatase


Mass: 19455.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 / Gene: HI_1679 / Plasmid: PDEST17-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45314, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO3
#4: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O8
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 30% polyethylene glycol 3350. Crystal soaked with 20 mM NaVN4, 20 mM KDO for 3 days. Crystal dragged through Paratone prior to flash cooling, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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: Jan 14, 2010 / 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: 1.8→29.5 Å / Num. obs: 14655 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rsym value: 0.0573 / Net I/σ(I): 13.68
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.3813 / % possible all: 91.4

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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 1k1e

1k1e


Resolution: 1.8→29.463 Å / σ(F): 1.38 / Phase error: 27.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1732 775 5.29 %
Rwork0.1467 --
obs0.1502 14655 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 21 177 1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141414
X-RAY DIFFRACTIONf_angle_d1.1361916
X-RAY DIFFRACTIONf_dihedral_angle_d14.838501
X-RAY DIFFRACTIONf_chiral_restr0.067221
X-RAY DIFFRACTIONf_plane_restr0.003241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.94040.31661450.25322617X-RAY DIFFRACTION86
1.9404-2.13550.27031300.19692652X-RAY DIFFRACTION87
2.1355-2.4440.18611450.1662781X-RAY DIFFRACTION91
2.444-3.07730.17171510.14582891X-RAY DIFFRACTION95
3.0773-19.96270.12791670.10922937X-RAY DIFFRACTION95

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