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- PDB-2r8x: Crystal structure of YrbI phosphatase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2r8x
TitleCrystal structure of YrbI phosphatase from Escherichia coli
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / YrbI / phosphatase KDO8-P
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 / 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: 2.6 Å
AuthorsTsodikov, O.V. / Aggarwal, P. / Rubin, J.R. / Stuckey, J.A. / Woodard, R.W. / 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
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
I: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
J: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
K: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
L: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
M: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
N: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
O: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
P: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,72020
Polymers320,57816
Non-polymers1424
Water12,358686
1
M: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
N: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

O: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
P: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

I: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
J: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
K: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
L: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)160,2898
Polymers160,2898
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
Buried area21600 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
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)160,43112
Polymers160,2898
Non-polymers1424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22000 Å2
MethodPISA
3
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)80,2517
Polymers80,1444
Non-polymers1063
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
MethodPISA
4
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)80,1805
Polymers80,1444
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
MethodPISA
5
I: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
J: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
K: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
L: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)80,1444
Polymers80,1444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
MethodPISA
6
M: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
N: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

O: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
P: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)80,1444
Polymers80,1444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.071, 156.959, 114.407
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21List of strains of Escherichia coli / Gene: yrbI / Plasmid details: pET / Production host: Escherichia coli (E. coli) / Strain (production host): B
References: UniProt: P67653, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→39.8 Å / Num. obs: 86138

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.725 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 4530 5 %RANDOM
Rwork0.20118 ---
obs0.20291 86138 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.34 Å2
2---0.48 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21566 0 4 686 22256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02221822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8641.99129595
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.97652873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79324.651860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.017153772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.71215142
X-RAY DIFFRACTIONr_chiral_restr0.0530.23561
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1550.210351
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.215062
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.21188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1961.514664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.362222726
X-RAY DIFFRACTIONr_scbond_it0.40838004
X-RAY DIFFRACTIONr_scangle_it0.7254.56869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 338 -
Rwork0.261 6132 -
obs--96.09 %
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)
11.40280.2702-0.36361.4624-0.24160.9404-0.04320.08120.1591-0.46260.11510.25040.0631-0.0908-0.0720.0668-0.0434-0.1468-0.12580.0748-0.040739.331112.2126-21.719
20.783-0.1075-0.45591.4193-0.21961.03640.009-0.03830.09230.0701-0.0154-0.02-0.11670.07030.0064-0.0733-0.0434-0.0232-0.1094-0.02580.012254.878919.23143.2363
30.57770.4569-0.03661.7145-0.92570.88810.0358-0.0505-0.1071-0.094-0.1777-0.40490.08110.09190.142-0.14720.0360.0137-0.0620.05380.110868.7591-7.53142.2673
41.89591.01320.01912.2073-0.54880.5814-0.15570.2047-0.186-0.70360.0593-0.15440.25310.04040.09650.2534-0.00660.0649-0.1262-0.0507-0.16153.2052-14.7112-22.7535
50.4360.3786-0.2721.9782-1.07081.50620.07020.06420.31610.01830.24590.8444-0.0266-0.175-0.3161-0.22720.01810.016-0.10420.13060.399714.83014.2635.8342
61.26640.2618-0.29361.251-0.5871.6953-0.05260.11620.0702-0.34460.2310.41040.3299-0.1455-0.17840.0174-0.1348-0.203-0.12910.08660.074720.9666-23.6799-5.7075
71.06440.033-0.23941.8587-0.36070.5540.089-0.0723-0.07670.1091-0.053-0.03480.11780.0376-0.036-0.02590.0012-0.0572-0.1040.0444-0.039140.4885-28.423115.8966
81.33190.94040.29912.5168-0.4610.89520.1829-0.17180.13070.5632-0.09530.2291-0.2219-0.004-0.08760.0584-0.03740.1252-0.0726-0.066-0.083435.0044-1.264927.8144
91.88520.5297-0.46331.824-0.09871.9904-0.1227-0.0033-0.0167-0.3201-0.1369-0.58-0.41960.25470.25960.1088-0.13360.28530.11010.15440.004614.4206-22.422347.3525
103.32550.2686-0.84981.7997-0.74151.3423-0.22450.2876-0.0641-1.07330.1018-0.42280.3293-0.00660.12270.5805-0.05670.42330.0779-0.0014-0.27572.268-43.926129.5666
112.08980.0323-0.74922.6106-0.71452.3553-0.1865-0.2128-0.5131-0.74660.1641-0.60830.54620.34950.02250.13770.2570.40020.05370.01050.098712.0872-65.331848.6304
122.0777-0.2587-0.31781.2131-0.11163.04470.0659-0.2285-0.2963-0.1669-0.2764-0.7997-0.09910.77030.2105-0.4169-0.02620.15840.49350.28270.282424.3246-43.896166.4375
131.94940.4811-0.18291.69660.10653.33030.05610.1522-0.28950.3716-0.0392-0.09160.69190.4015-0.0170.01650.1459-0.01640.0764-0.1142-0.138523.833718.0081-59.3893
141.48180.36790.1520.9923-0.33882.8072-0.07160.12620.01030.3743-0.0534-0.1469-0.28820.260.1250.0458-0.0525-0.10190.1704-0.0489-0.25726.897246.5596-49.7755
152.53730.9066-0.28421.7191-0.53742.17790.0665-0.3130.13950.1136-0.1654-0.0886-0.6645-0.12330.09890.10440.0339-0.03440.1378-0.0345-0.25160.9376-22.0517-39.6591
161.933-0.67010.20160.6768-0.23023.3918-0.0946-0.1266-0.0740.1554-0.0029-0.1320.10740.01460.0975-0.1336-0.012-0.01180.16960.1186-0.13784.3832-50.5443-29.9357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1888 - 188
2X-RAY DIFFRACTION2BB8 - 1888 - 188
3X-RAY DIFFRACTION3CC8 - 1888 - 188
4X-RAY DIFFRACTION4DD8 - 1888 - 188
5X-RAY DIFFRACTION5EE8 - 1888 - 188
6X-RAY DIFFRACTION6FF8 - 1798 - 179
7X-RAY DIFFRACTION7GG8 - 1888 - 188
8X-RAY DIFFRACTION8HH8 - 1888 - 188
9X-RAY DIFFRACTION9II8 - 1888 - 188
10X-RAY DIFFRACTION10JJ8 - 1888 - 188
11X-RAY DIFFRACTION11KK8 - 1888 - 188
12X-RAY DIFFRACTION12LL8 - 1888 - 188
13X-RAY DIFFRACTION13MM8 - 1888 - 188
14X-RAY DIFFRACTION14NN8 - 1888 - 188
15X-RAY DIFFRACTION15OO8 - 1888 - 188
16X-RAY DIFFRACTION16PP8 - 1888 - 188

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