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- PDB-3hyc: Crystal structure of E. coli phosphatase YrbI, with Mg, tetragona... -

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Basic information

Entry
Database: PDB / ID: 3hyc
TitleCrystal structure of E. coli phosphatase YrbI, with Mg, tetragonal form
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / YrbI / KdsC / 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-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsTsodikov, O.V. / Biswas, T.
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
DepositionJun 22, 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 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
F: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
G: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
H: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,66121
Polymers160,2898
Non-polymers37213
Water00
1
E: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
F: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
G: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
H: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34811
Polymers80,1444
Non-polymers2047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-116 kcal/mol
Surface area25010 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


Theoretical massNumber of molelcules
Total (without water)80,31310
Polymers80,1444
Non-polymers1686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-104 kcal/mol
Surface area25280 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22510 Å2
ΔGint-256 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.219, 122.219, 202.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 20036.121 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Gene: YrbI
References: UniProt: P67653, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris propane pH 6.0, 100 mM NaCl, 13.5 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 3.06→48.08 Å / Num. obs: 29776

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8E

2r8e


Resolution: 3.06→48.08 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.89 / SU B: 44.21 / SU ML: 0.358 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1485 5.1 %RANDOM
Rwork0.24164 ---
obs0.24239 27820 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.555 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---1.22 Å20 Å2
3---2.44 Å2
Refinement stepCycle: LAST / Resolution: 3.06→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10784 0 13 0 10797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.981.99414795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75751428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63124.691437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1731572
X-RAY DIFFRACTIONr_chiral_restr0.0650.21780
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218036
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.041.57084
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.084211313
X-RAY DIFFRACTIONr_scbond_it0.18433828
X-RAY DIFFRACTIONr_scangle_it0.3264.53482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.06→3.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 87 -
Rwork0.306 2006 -
obs--97.53 %
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)
12.3336-0.04280.3290.6259-0.35353.35190.0672-0.35210.00140.18260.04690.3056-0.0874-0.2432-0.11410.10950.00330.06590.06880.01230.161327.897622.3229-24.9994
22.1563-0.8090.01273.7459-0.86942.23870.1269-0.28970.48170.3059-0.0825-0.1989-0.45090.2163-0.04440.1326-0.04930.01070.0916-0.09440.139349.678742.4791-27.1002
32.15720.0739-1.21862.8035-1.28932.88270.0364-0.0120.0617-0.03740.012-0.2868-0.00390.3054-0.04840.02420.0056-0.00940.0583-0.03180.052862.933326.4015-50.068
43.00540.12780.95922.3455-0.24363.67150.0330.0861-0.4147-0.1249-0.03110.19390.4107-0.1311-0.00190.1207-0.0011-0.0220.0142-0.02790.09241.01426.1466-47.7576
51.37750.47360.38581.6404-1.22134.0347-0.01920.08870.1665-0.09290.04640.632-0.1804-0.8716-0.02720.09820.0296-0.14370.3801-0.02870.44427.902132.7415-55.4193
63.2632-0.54670.38642.9657-0.8542.4599-0.04750.83140.023-0.75830.08310.23060.1789-0.0691-0.03560.3663-0.0456-0.15520.3308-0.00910.075628.937827.5112-76.3837
74.8627-1.0536-0.09333.434-1.09140.76820.05180.62720.7005-0.4642-0.0919-0.1765-0.19840.03160.04010.4114-0.0127-0.03020.1930.0990.276943.408553.0988-68.7243
82.2057-0.39760.29482.2679-0.44832.33140.0833-0.04010.46960.136-0.00590.2937-0.2316-0.3765-0.07740.17740.0788-0.07440.1135-0.06120.438522.320658.3886-47.7816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 188
2X-RAY DIFFRACTION2B8 - 181
3X-RAY DIFFRACTION3C8 - 188
4X-RAY DIFFRACTION4D8 - 183
5X-RAY DIFFRACTION5E8 - 188
6X-RAY DIFFRACTION6F8 - 188
7X-RAY DIFFRACTION7G8 - 188
8X-RAY DIFFRACTION8H8 - 188

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