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- PDB-1k1e: Structure Of the cobalt-bound form of the deoxy-D-mannose-octulos... -

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Basic information

Entry
Database: PDB / ID: 1k1e
TitleStructure Of the cobalt-bound 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 / MOLECULAR REPLACEMENT / Resolution: 1.67 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
DepositionSep 25, 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 1.3Aug 16, 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_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 / _struct_conn.ptnr2_label_seq_id / _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
E: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
F: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
G: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
H: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
I: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
J: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
K: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
L: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,44563
Polymers233,46312
Non-polymers5,98251
Water25,4731414
1
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)79,81521
Polymers77,8214
Non-polymers1,99417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-176 kcal/mol
Surface area23830 Å2
MethodPISA
2
E: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
F: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
G: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
H: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,72320
Polymers77,8214
Non-polymers1,90216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-177 kcal/mol
Surface area23750 Å2
MethodPISA
3
I: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
J: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
K: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
L: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,90722
Polymers77,8214
Non-polymers2,08618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-176 kcal/mol
Surface area23940 Å2
MethodPISA
4
I: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
J: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
K: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
L: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules

I: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
J: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
K: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
L: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,81444
Polymers155,6428
Non-polymers4,17236
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27190 Å2
ΔGint-369 kcal/mol
Surface area44020 Å2
MethodPISA
5
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
E: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
F: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
G: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
H: deoxy-D-mannose-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,53841
Polymers155,6428
Non-polymers3,89633
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26900 Å2
ΔGint-367 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.3, 109.1, 179.1
Angle α, β, γ (deg.)90.0, 107.6, 90.0
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a tetramer. The asymmetric unit contains three tetramers

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 19455.283 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI1679 / Plasmid: PDEST17-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): B21(DE3)
References: UniProt: P45314, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 6 types, 1465 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1414 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M ammonium sulfate, 0.1 M MES, 10 mM CoCl2. Crystal soaked with 1mM Hg acetate for 3 days. 10% glycerol added for flash-cooling, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Aug 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 199616 / Num. obs: 199616 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 1.67→1.75 Å / Rmerge(I) obs: 0.213 / % possible all: 49.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HI1679 (PDB code 1j8d)

1j8d


Resolution: 1.67→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 11439 -random
Rwork0.178 ---
obs-190806 82.5 %-
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.67→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15793 0 186 1414 17393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.021
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 1.67→1.75 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.206

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