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- PDB-4jb3: Crystal structure of BT_0970, a had family phosphatase from bacte... -

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Basic information

Entry
Database: PDB / ID: 4jb3
TitleCrystal structure of BT_0970, a had family phosphatase from bacteroides thetaiotaomicron VPI-5482, TARGET EFI-501083, with bound sodium and glycerol, closed lid, ordered loop
ComponentsHaloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / HAD / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase / 5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity / ribitol-5-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / riboflavin biosynthetic process / dephosphorylation / metal ion binding
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-ribitol-5-phosphate phosphatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Kumar, P.R. / Ghosh, A. / Al Obaidi, N.F. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Kumar, P.R. / Ghosh, A. / Al Obaidi, N.F. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of bt_0970, a had family phosphatase from bacteroides thetaiotaomicron VPI-5482, TARGET EFI-501083, with bound sodium and glycerol, closed lid, ordered loop
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Kumar, P.R. / Ghosh, A. / Al Obaidi, N.F. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Kumar, P.R. / Ghosh, A. / Al Obaidi, N.F. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2443
Polymers26,1291
Non-polymers1152
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.580, 91.190, 46.270
Angle α, β, γ (deg.)90.000, 104.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein Haloacid dehalogenase-like hydrolase


Mass: 26129.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_0970 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A947
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 298 K / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM DTT); Reservoir (2.4 M Sodium Malonate pH 7.0); Cryoprotection (Reservoir, 20% glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: RAYONIX 225 HE / Detector: CCD / Date: Jan 24, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→42.517 Å / Num. all: 30037 / Num. obs: 30037 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 14.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3217 / Rsym value: 0.3 / % possible all: 69.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I6X

2i6x


Resolution: 1.5→42.517 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.9048 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 16.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1717 1519 5.06 %RANDOM
Rwork0.146 ---
all0.1473 30033 --
obs0.1473 30033 94.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.51 Å2 / Biso mean: 18.0384 Å2 / Biso min: 5.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 7 211 1976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091840
X-RAY DIFFRACTIONf_angle_d1.0652495
X-RAY DIFFRACTIONf_chiral_restr0.076267
X-RAY DIFFRACTIONf_plane_restr0.005325
X-RAY DIFFRACTIONf_dihedral_angle_d12.984676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.54840.23611040.17431792189665
1.5484-1.60380.20321150.15812172228779
1.6038-1.6680.1821420.15692580272295
1.668-1.74390.16721510.146527222873100
1.7439-1.83590.16521410.145527522893100
1.8359-1.95090.17651480.144427352883100
1.9509-2.10150.171460.141227582904100
2.1015-2.3130.16831450.136327282873100
2.313-2.64760.1811450.152737288299
2.6476-3.33550.16891440.151327602904100
3.3355-42.53430.15941380.14142778291699
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)
12.2319-0.2696-0.52075.10251.23212.95510.04880.0765-0.0742-0.0853-0.10780.0851-0.0035-0.0960.05060.0421-0.0035-0.01460.05740.00260.037911.087198.66668.3002
22.23120.3989-0.79597.6046-1.26865.36820.04880.1780.0414-0.6406-0.0239-0.04970.23780.1878-0.0010.17270.0144-0.03150.0922-0.03890.10713.913375.46092.5587
31.8161-2.165-0.70995.4471.00791.44760.07970.37670.0679-0.2391-0.10610.5348-0.0128-0.26140.00190.1708-0.0274-0.03690.194-0.01590.19915.076377.47755.489
41.8374-0.3890.68814.2846-0.15152.21350.0532-0.0767-0.0963-0.08990.04870.31410.2206-0.1848-0.06370.0947-0.014-0.00060.07570.0140.08978.404374.785617.7166
52.80240.43240.65684.055-0.61122.853-0.0202-0.0839-0.0346-0.0951-0.1346-0.3820.30340.12080.09610.11940.00730.00760.0789-0.02750.085718.095474.596612.242
62.02690.7059-0.70821.2548-0.68641.97480.002-0.0995-0.10690.0468-0.0494-0.19420.0980.1067-00.0584-0.0046-0.01410.10830.01930.091820.2339100.08616.3723
70.6403-0.50850.08171.5944-0.60510.8210.0256-0.04780.05530.0387-0.0601-0.1042-0.07040.00490.03960.08390.00350.00080.0687-0.0080.090513.964693.953815.0587
85.1734-0.0423-1.5271.05361.37865.8855-0.0547-0.09140.09580.0018-0.0898-0.19560.03210.6550.10130.06160.0176-0.00450.16830.0570.112126.240293.292712.8797
90.34470.49730.0240.7779-0.22530.37040.0019-0.09320.04360.0829-0.0769-0.0609-0.07030.06260.06950.10220.0013-0.02050.0917-0.00480.094914.064595.624718.933
100.55650.83530.83593.55781.70521.3081-0.1866-0.16490.02620.25370.14410.4501-0.1387-0.30160.06450.12710.07210.04370.16730.00660.061.35595.631719.7459
112.18650.09150.10273.05421.8212.9040.0448-0.027-0.01020.2591-0.02110.08550.0967-0.1386-0.01870.05490.0061-0.00190.06150.01090.0360.9019101.199610.9239
121.62670.6186-0.78570.8709-0.70881.51720.0620.02850.09620.009-0.04660.0501-0.147-0.0984-0.02030.06430.0203-0.00790.08880.00730.0698.0704104.17222.4564
131.3461-0.7855-2.00883.13820.9923.2360.581-0.14340.67880.72270.1182-0.4334-0.43820.5027-0.65670.8129-0.00110.04020.4783-0.02320.836117.8673114.15882.8354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 28 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 43 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 67 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 83 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 84 through 100 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 118 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 119 through 129 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 130 through 143 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 144 through 160 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 161 through 182 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 183 through 206 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid -11 through 0 )A0

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