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- PDB-6e4b: The crystal structure of a putative alpha-ribazole-5'-P phosphata... -

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Basic information

Entry
Database: PDB / ID: 6e4b
TitleThe crystal structure of a putative alpha-ribazole-5'-P phosphatase from Escherichia coli str. K-12 substr. MG1655
ComponentsAdenosylcobalamin/alpha-ribazole phosphatase
KeywordsHYDROLASE / alpha-ribazole-5'-P phosphatase / Center For Structural Genomics Of Infectious Diseases (CSGID)
Function / homology
Function and homology information


adenosylcobalamin/alpha-ribazole phosphatase / alpha-ribazole phosphatase activity / cobalamin biosynthetic process / phosphatase activity / cytoplasm
Similarity search - Function
Alpha-ribazole phosphatase, CobC / : / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold ...Alpha-ribazole phosphatase, CobC / : / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenosylcobalamin/alpha-ribazole phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTan, K. / Maltseva, N. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of a putative alpha-ribazole-5'-P phosphatase from Escherichia coli str. K-12 substr. MG1655 (CASP target)
Authors: Tan, K. / Maltseva, N. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Adenosylcobalamin/alpha-ribazole phosphatase
B: Adenosylcobalamin/alpha-ribazole phosphatase
C: Adenosylcobalamin/alpha-ribazole phosphatase
D: Adenosylcobalamin/alpha-ribazole phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,99310
Polymers104,3174
Non-polymers6756
Water1,24369
1
A: Adenosylcobalamin/alpha-ribazole phosphatase
B: Adenosylcobalamin/alpha-ribazole phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8348
Polymers52,1592
Non-polymers6756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-47 kcal/mol
Surface area17260 Å2
MethodPISA
2
C: Adenosylcobalamin/alpha-ribazole phosphatase
D: Adenosylcobalamin/alpha-ribazole phosphatase


Theoretical massNumber of molelcules
Total (without water)52,1592
Polymers52,1592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-6 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.114, 53.772, 199.133
Angle α, β, γ (deg.)90.00, 98.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Adenosylcobalamin/alpha-ribazole phosphatase / Adenosylcobalamin phosphatase / Alpha-ribazole-5'-phosphate phosphatase


Mass: 26079.373 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: cobC, phpB, b0638, JW0633 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: P52086, adenosylcobalamin/alpha-ribazole phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris base/Hydrochloric acid. 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationMonochromator: Si crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→46.5 Å / Num. obs: 38300 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 31.91 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.064 / Rrim(I) all: 0.118 / Χ2: 0.874 / Net I/σ(I): 12.65
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1779 / CC1/2: 0.564 / Rpim(I) all: 0.518 / Rrim(I) all: 0.891 / Χ2: 0.851 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJ5

4ij5


Resolution: 2.55→46.172 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1663 4.99 %random
Rwork0.1932 ---
obs0.1949 33309 84.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 41 69 6329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026406
X-RAY DIFFRACTIONf_angle_d0.4498702
X-RAY DIFFRACTIONf_dihedral_angle_d10.8584128
X-RAY DIFFRACTIONf_chiral_restr0.04962
X-RAY DIFFRACTIONf_plane_restr0.0021132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.62510.374650.27041315X-RAY DIFFRACTION42
2.6251-2.70990.3298920.26551676X-RAY DIFFRACTION54
2.7099-2.80670.26661080.25262007X-RAY DIFFRACTION65
2.8067-2.91910.29491300.23582381X-RAY DIFFRACTION77
2.9191-3.05190.28551420.2362661X-RAY DIFFRACTION86
3.0519-3.21280.26191430.22283000X-RAY DIFFRACTION95
3.2128-3.4140.24991420.20553047X-RAY DIFFRACTION97
3.414-3.67750.21891680.1813063X-RAY DIFFRACTION98
3.6775-4.04740.18421690.16693043X-RAY DIFFRACTION98
4.0474-4.63260.17491750.15183112X-RAY DIFFRACTION99
4.6326-5.83470.21091660.18153142X-RAY DIFFRACTION98
5.8347-46.17950.23671630.19453199X-RAY DIFFRACTION98
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)
10.60710.0373-0.03081.1137-0.36760.43630.023-0.0679-0.02020.1311-0.0997-0.18880.08440.06720.06780.13750.01970.0598-0.01460.11640.314920.16170.12717.7613
20.717-0.1525-0.43111.2680.2460.9412-0.1591-0.0572-0.36460.0884-0.0982-0.15170.28390.091-0.46650.22580.10770.06230.09020.07850.398621.6943-12.33869.9724
31.7484-0.235-0.53480.8143-0.93152.1247-0.04770.185-0.36-0.3243-0.0402-0.10080.54-0.13570.01780.18680.02130.0281-0.03090.02410.342310.9393-7.04493.0622
41.2010.866-0.23930.739-0.11280.42320.2476-0.1223-0.07270.267-0.0838-0.1185-0.27650.07160.34790.208-0.06020.142-0.04550.1460.284223.348712.73163.6958
56.17572.3198-1.69062.21510.86434.10870.1808-0.47460.30090.5007-0.2046-0.1982-0.38220.10040.0450.3721-0.1440.0190.19680.03020.322829.80620.88979.8994
61.89991.95391.74065.94131.79741.59630.1663-0.34180.31740.854-0.24210.63780.1962-0.29940.13320.45560.01770.11360.101-0.03510.398917.742620.53538.9244
73.54482.91530.05214.2430.27262.0063-0.04620.09460.6105-0.1951-0.02190.6879-0.3106-0.48890.10650.15430.072-0.02810.2240.01390.2214.24319.23977.558
82.1268-0.11980.60210.6872-0.03040.9814-0.134-0.0041-0.1204-0.05050.09020.39850.2748-0.3415-0.27980.1075-0.09220.04390.0910.06820.33493.1792-4.86518.0794
91.98220.455-0.99336.183-0.03763.25420.0924-0.08990.4080.19430.0343-0.2303-0.26360.0035-0.01320.06150.03350.02230.0430.03170.20949.71626.2514.9311
102.7364-0.0351-1.64475.12031.25332.110.027-0.35880.43090.33640.1659-0.5704-0.03830.2685-0.1740.1545-0.0892-0.02820.2513-0.03130.187913.81315.07119.0225
115.8395-4.4692-0.47494.47080.22762.15-0.03140.0049-0.6626-0.0871-0.11080.59470.2392-0.17320.09180.0894-0.03930.01550.24430.16080.33425.198-5.529219.6762
123.69170.5329-0.33721.8657-0.10332.50930.0062-0.6691-0.29240.1785-0.2843-0.06930.48340.45560.23350.3506-0.01810.05080.48550.22840.279711.22-11.338838.6259
132.11190.6096-1.04016.10311.36714.25160.149-0.9502-0.20520.7604-0.0876-0.53690.64170.7581-0.04190.3933-0.0346-0.07210.69820.22580.280316.3701-9.845145.1162
140.93190.51940.09140.5150.02920.0105-0.0505-0.3807-0.03680.0158-0.16190.02750.3994-0.12430.16960.4235-0.21880.10070.65420.01480.2962-5.5196-5.355445.24
155.27864.1803-0.67175.7543-2.40381.7080.21360.13870.7264-0.04380.01410.8211-0.0265-0.5243-0.16430.3126-0.05440.10240.79670.01150.4731-12.9028-0.411640.7705
163.3870.19180.961.0292-0.67070.79150.0966-0.65240.37850.3962-0.1993-0.1661-0.32850.53280.14830.3697-0.2204-0.04810.75670.0190.153413.52514.619241.736
174.5078-1.80871.29423.9698-1.64415.78230.1027-0.3292-0.02870.27970.11170.1334-0.2795-0.0454-0.02230.2126-0.09150.0150.3603-0.00250.12735.21664.708432.2874
182.7826-1.0378-0.37237.1021-0.32922.75390.093-0.8921-0.2585-0.0049-0.1918-0.3862-0.01260.6439-0.00130.1901-0.0689-0.02470.41230.10310.21916.1222-2.131528.5407
192.84930.7399-0.54695.3841-1.69463.06230.15910.07860.11310.0403-0.0704-0.1922-0.03770.1768-0.08740.2902-0.1732-0.00180.77540.00610.147334.29111.490154.8536
202.2418-1.766-0.74422.92162.3044.09350.3445-0.19761.02280.6787-0.06810.8158-0.9549-0.5625-0.25940.86310.06650.16720.74090.04840.876521.339330.874561.6724
212.50830.7766-0.82926.04340.09331.9334-0.0473-0.03070.0072-0.15950.25230.87380.3932-0.9079-0.15390.4356-0.2495-0.07571.02870.11960.233820.02547.24157.9185
223.1645-0.12810.47593.3225-2.12764.37390.1657-0.57760.10140.60180.0530.2482-0.2509-0.2846-0.21520.587-0.12490.00090.8605-0.00120.193127.31058.336868.3592
231.3172-0.4705-0.92562.2119-0.66524.2651-0.3594-0.1967-0.24850.49080.1213-0.13021.2080.39850.1991.35860.0672-0.24451.04520.00650.386540.2883-3.429184.3463
240.33140.0921-0.32211.1902-0.84452.0976-0.0499-0.4375-0.07340.3413-0.1556-0.19660.49270.3869-0.08551.27180.0763-0.39251.1794-0.01630.311843.90474.44590.6087
250.025-0.0507-0.01330.22540.16880.16620.3983-0.2794-0.56741.04410.1409-0.1579-0.5247-0.151-0.25111.4377-0.3084-0.22691.36940.19630.724227.1667-11.561993.2633
260.0126-0.022-0.00260.04310.00440.00030.2301-0.2533-0.0911.151-0.1656-0.292-1.007-0.0684-0.08181.6358-0.20310.18771.5244-0.0361.153718.0672-17.797688.213
274.05441.48440.64273.39491.38820.9557-0.2514-0.5763-0.31640.61690.07950.2360.3401-0.43850.12911.2937-0.02590.15561.31910.06170.284522.65621.458992.5708
281.9934-0.4381-1.41861.2395-0.67541.8538-0.036-0.47830.11791.05870.00650.0079-0.0149-0.1378-0.01940.98040.0135-0.06181.1831-0.04580.092632.01177.923981.1255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 108 )
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 138 )
8X-RAY DIFFRACTION8chain 'A' and (resid 139 through 149 )
9X-RAY DIFFRACTION9chain 'A' and (resid 150 through 160 )
10X-RAY DIFFRACTION10chain 'A' and (resid 161 through 178 )
11X-RAY DIFFRACTION11chain 'A' and (resid 179 through 202 )
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 55 )
13X-RAY DIFFRACTION13chain 'B' and (resid 56 through 79 )
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 91 )
15X-RAY DIFFRACTION15chain 'B' and (resid 92 through 120 )
16X-RAY DIFFRACTION16chain 'B' and (resid 121 through 149 )
17X-RAY DIFFRACTION17chain 'B' and (resid 150 through 170 )
18X-RAY DIFFRACTION18chain 'B' and (resid 171 through 202 )
19X-RAY DIFFRACTION19chain 'C' and (resid -1 through 79 )
20X-RAY DIFFRACTION20chain 'C' and (resid 80 through 120 )
21X-RAY DIFFRACTION21chain 'C' and (resid 121 through 149 )
22X-RAY DIFFRACTION22chain 'C' and (resid 150 through 201 )
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 41 )
24X-RAY DIFFRACTION24chain 'D' and (resid 42 through 79 )
25X-RAY DIFFRACTION25chain 'D' and (resid 80 through 91 )
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 108 )
27X-RAY DIFFRACTION27chain 'D' and (resid 109 through 135 )
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 200 )

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