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- PDB-1j8d: Structure Of the metal-free form of the deoxy-D-mannose-octuloson... -

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Basic information

Entry
Database: PDB / ID: 1j8d
TitleStructure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)
Componentsdeoxy-D-mannose-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / HI1679 / structural genomics / KDO 8-P phosphatase / Structure 2 Function Project / S2F
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-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLim, K. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2002
Title: From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.
Authors: Parsons, J.F. / Lim, K. / Tempczyk, A. / Krajewski, W. / Eisenstein, E. / Herzberg, O.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400COMPOUND THE FUNCTION OF THE PROTEIN WAS ASSIGNED INDEPENDENTLY BY THE WOODARD GROUP: ESCHERICHIA ...COMPOUND THE FUNCTION OF THE PROTEIN WAS ASSIGNED INDEPENDENTLY BY THE WOODARD GROUP: ESCHERICHIA COLI YRBI IS 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE, WU J, WOODARD RW; J BIOL CHEM. 2003 278:18117-2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
B: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
C: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
D: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2265
Polymers79,1344
Non-polymers921
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-28 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.77, 132.30, 140.97
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
deoxy-D-mannose-octulosonate 8-phosphate phosphatase / YRBI / KDO 8-P Phosphatase / HI1679


Mass: 19783.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI1679 / Plasmid: pDEST14-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P45314, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: protein (10 mg/ml) in 10mM NaHepes, pH 7.5, 1mM EDTA, 1mM DTT; crystallization in 22% polyethylene glycol 4000, 0.1 M Tris-HCl, 0.2 M Lithium sulfate. Glycerol added as cryoprotectant., pH 8. ...Details: protein (10 mg/ml) in 10mM NaHepes, pH 7.5, 1mM EDTA, 1mM DTT; crystallization in 22% polyethylene glycol 4000, 0.1 M Tris-HCl, 0.2 M Lithium sulfate. Glycerol added as cryoprotectant., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 36 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
122 %(w/v)PEG40001reservoir
20.2 M1reservoirLi2SO4
30.1 MTris-HCl1reservoirpH8.5
429 mg/mlprotein1drop
510 mMHEPES1droppH7.5
650 mM1NaCl
71 mMEDTA1drop
81 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9790, 0.9787, 0.9500
DetectorType: BRANDEIS / Detector: CCD / Date: Aug 20, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97871
30.951
ReflectionResolution: 2.3→50 Å / Num. all: 28788 / Num. obs: 28788 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.171 / Num. unique all: 3494 / % possible all: 95.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 158161
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 95.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
MLPHAREphasing
DMmodel building
CNSrefinement
SHELXphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1581 5.9 %random
Rwork0.176 ---
all-27928 --
obs-26906 --
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 6 259 5713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.3→2.38 Å /
Rfactor% reflection
Rfree0.302 -
Rwork0.198 -
obs-95.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.9 % / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.198

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