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- PDB-3i6b: Crystal structure of YrbI lacking the last 8 residues, in complex... -

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Basic information

Entry
Database: PDB / ID: 3i6b
TitleCrystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / YrbI / KdsC / Kdo / phosphatase / Lipopolysaccharide biosynthesis / Magnesium
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / N-acylneuraminate cytidylyltransferase activity / lipopolysaccharide biosynthetic process / 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
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / PHOSPHATE ION / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsBiswas, T. / Tsodikov, O.V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE.
Authors: Biswas, T. / Yi, L. / Aggarwal, P. / Wu, J. / Rubin, J.R. / Stuckey, J.A. / Woodard, R.W. / Tsodikov, O.V.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,77814
Polymers76,8254
Non-polymers95310
Water3,387188
1
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,77814
Polymers76,8254
Non-polymers95310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-106 kcal/mol
Surface area24690 Å2
MethodPISA
2
A: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
B: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
C: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
D: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)155,55728
Polymers153,6508
Non-polymers1,90720
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area25250 Å2
ΔGint-248 kcal/mol
Surface area44920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.964, 144.104, 145.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 19206.242 Da / Num. of mol.: 4 / Fragment: Residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Gene: c3958, kdsC, YrbI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67653, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#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.: 2
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.: 188 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 1.875 M Ammonium Sulfate, 100mM Na Cacodylate pH 6.5, 2.5% glycerol, stoichiometric amount of Kdo8P (cleaved upon incubation in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.06699
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.06699 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 21494 / % possible obs: 92.7 % / Observed criterion σ(I): 2.3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.9
Reflection shellResolution: 2.49→2.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE: 2R8E

2r8e


Resolution: 2.49→40 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.357 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1132 5 %RANDOM
Rwork0.2 ---
obs0.202 21494 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.34 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.17 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.49→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 56 188 5442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0722.0027213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8555694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42124.4200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72715903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9651534
X-RAY DIFFRACTIONr_chiral_restr0.0710.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023858
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22496
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23643
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4911.53534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63325491
X-RAY DIFFRACTIONr_scbond_it1.13731976
X-RAY DIFFRACTIONr_scangle_it1.7994.51722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 87 -
Rwork0.248 1600 -
obs--94.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.346-0.39560.29631.823-0.32291.02350.01580.0301-0.0014-0.0171-0.01280.06870.008-0.0539-0.003-0.0618-0.0173-0.0041-0.03820.0028-0.087514.6515-15.7209-15.2979
20.86910.7163-0.43932.332-0.2412.01830.02070.0673-0.1499-0.1094-0.0169-0.09780.04720.0971-0.0038-0.11680.0197-0.0001-0.015-0.0151-0.030244.2419-14.6004-20.9276
31.216-0.290.36241.67360.36181.1647-0.046-0.0742-0.0275-0.00530.0321-0.1550.00730.01680.0139-0.07790.00610.0024-0.06390.0085-0.07849.5177-20.07698.9744
40.7694-0.3574-0.53591.82620.55941.3514-0.0117-0.0121-0.10450.078-0.01310.09010.0806-0.01620.0248-0.0763-0.014-0.0043-0.01990.0165-0.035820.0058-20.914614.6451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 179
2X-RAY DIFFRACTION1B900
3X-RAY DIFFRACTION2B6 - 180
4X-RAY DIFFRACTION3C6 - 180
5X-RAY DIFFRACTION3D900
6X-RAY DIFFRACTION4D6 - 180

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