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- PDB-2r8z: Crystal structure of YrbI phosphatase from Escherichia coli in co... -

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Basic information

Entry
Database: PDB / ID: 2r8z
TitleCrystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion
Components3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
KeywordsHYDROLASE / YrbI / phosphatase / divalent metal / phosphate / KDO8-P / HAD superfamily / Lipopolysaccharide biosynthesis / Magnesium
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase activity / 3-deoxy-manno-octulosonate-8-phosphatase / 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
PHOSPHATE ION / 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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_asym_id / _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_asym_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_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 / _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)322,73948
Polymers320,57816
Non-polymers2,16132
Water46,8032598
1
M: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
N: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules

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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,36924
Polymers160,2898
Non-polymers1,08016
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_545-x,y-1/2,-z1
identity operation1_555x,y,z1
Buried area24020 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)161,36924
Polymers160,2898
Non-polymers1,08016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23910 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)80,68512
Polymers80,1444
Non-polymers5408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
MethodPISA
4
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,68512
Polymers80,1444
Non-polymers5408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
MethodPISA
5
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)80,68512
Polymers80,1444
Non-polymers5408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
MethodPISA
6
M: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
N: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
hetero molecules

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)80,68512
Polymers80,1444
Non-polymers5408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.370, 156.908, 114.051
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
Details: pET / Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: BL21 / Gene: kdsC / Production host: Escherichia coli (E. coli) / Strain (production host): B
References: UniProt: P67653, 3-deoxy-manno-octulosonate-8-phosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2598 / 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: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→38.4 Å / Num. obs: 162029

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.433 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23075 8524 5 %RANDOM
Rwork0.18397 ---
obs0.1863 162029 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å21.06 Å2
2---0.3 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21648 0 96 2598 24342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02221968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0452.01829790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.70452874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38424.715878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.143153814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.16815144
X-RAY DIFFRACTIONr_chiral_restr0.0660.23560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.211965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.215098
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.22606
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.282
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.2151
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2951.514702
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.535222746
X-RAY DIFFRACTIONr_scbond_it0.87738144
X-RAY DIFFRACTIONr_scangle_it1.4284.57044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 533 -
Rwork0.242 10595 -
obs--87.16 %
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)
11.93470.13720.00780.9056-0.08590.9116-0.04270.1630.0979-0.19680.02130.0905-0.0516-0.03060.0213-0.102-0.0032-0.0762-0.14960.0316-0.170539.63112.344-21.635
21.49890.79350.06951.8668-0.11230.7144-0.00530.2112-0.1658-0.23180.0361-0.130.09230.1029-0.0308-0.11380.029-0.0192-0.078-0.0665-0.167753.57-14.428-22.787
30.89160.138-0.09721.3664-0.62021.15250.03620.023-0.06280.0832-0.0784-0.2731-0.00670.11120.0422-0.21060.016-0.077-0.1525-0.0111-0.049269.013-7.4372.327
40.99330.0618-0.22810.96910.17421.0139-0.02390.02730.06520.0376-0.00470.0024-0.1301-0.00610.0286-0.1519-0.0187-0.0619-0.1818-0.0015-0.121755.06319.253.557
51.06260.0764-0.34251.07060.0511.36010.05630.1212-0.0247-0.0571-0.00740.15650.0827-0.0983-0.0489-0.1499-0.0291-0.0974-0.16720.0221-0.139820.957-23.316-6.385
60.99750.09460.07851.3976-0.35761.04940.0228-0.03590.14390.0678-0.00180.2154-0.0421-0.0896-0.021-0.21070.0172-0.031-0.13890.0095-0.064114.884.0875.607
71.79290.640.08461.6042-0.1180.6248-0.0185-0.27460.09440.25050.022-0.0241-0.0517-0.0705-0.0035-0.10370.0333-0.0337-0.0968-0.0381-0.190634.758-1.52327.729
81.4246-0.3285-0.29870.94610.04241.02740.0363-0.0394-0.12060.14050.0484-0.06190.2209-0.0265-0.0847-0.0712-0.0083-0.1095-0.17340.0317-0.158140.702-28.51815.654
92.90250.1986-0.13551.259-0.13971.8868-0.16070.2607-0.1216-0.55160.106-0.1497-0.0823-0.27250.05470.2215-0.02090.10710.0140.0158-0.17451.542-43.96328.999
102.11910.283-0.61081.48080.11742.0216-0.0643-0.0941-0.349-0.17420.0271-0.30250.3123-0.01550.03720.01750.02330.1518-0.06280.04780.087511.566-65.35747.863
111.6566-0.1115-0.91611.40490.30593.15920.0219-0.3498-0.16460.0229-0.0566-0.5084-0.20920.44620.0348-0.1339-0.0184-0.00040.13450.12240.117924.071-44.00565.413
122.3006-0.249-0.63671.3584-0.22192.3792-0.0284-0.03060.1580.0296-0.0149-0.209-0.67280.03510.04330.231-0.02010.0814-0.05230.0486-0.053814.139-22.63446.481
132.30460.8404-0.50072.1069-0.41481.59150.1264-0.29420.12890.0982-0.1971-0.1179-0.5386-0.25510.07070.14860.2005-0.01530.1680.0193-0.22390.924-22.195-39.71
141.2946-0.3754-0.13131.22810.09522.213-0.02910.07-0.0650.0776-0.0307-0.12560.107-0.20540.0599-0.1325-0.0153-0.04540.14560.0701-0.19414.392-50.775-30.203
151.42050.1716-0.66011.8758-0.51932.3836-0.03060.0677-0.2430.1721-0.0335-0.09970.31730.66040.0641-0.06980.1499-0.04620.3682-0.045-0.191624.04717.707-59.176
161.45330.1102-0.39921.4001-0.40661.81930.1569-0.16680.04640.3289-0.1783-0.1102-0.3730.62220.02140.0992-0.2888-0.12670.4633-0.0422-0.288727.44846.583-49.557
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 - 1858 - 185
6X-RAY DIFFRACTION6FF8 - 1888 - 188
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 - 1858 - 185
16X-RAY DIFFRACTION16PP8 - 1888 - 188

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