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- PDB-4c1r: Bacteroides thetaiotaomicron VPI-5482 mannosyl-6-phosphatase Bt3783 -

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Basic information

Entry
Database: PDB / ID: 4c1r
TitleBacteroides thetaiotaomicron VPI-5482 mannosyl-6-phosphatase Bt3783
ComponentsMANNOSYL-6-PHOSPHATASE
KeywordsHYDROLASE / GUT MICROBIOTA
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity / endonuclease activity / metal ion binding
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Endonuclease/exonuclease/phosphatase family protein
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. ...Cuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. / Suits, M.D.L. / Boraston, A.B. / Williams, S.J. / Davies, G.J. / Abbott, W.D. / Martens, E.C. / Gilbert, H.J.
CitationJournal: Nature / Year: 2015
Title: Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.
Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, ...Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, T.J. / Piens, K. / Bracke, D. / Vervecken, W. / Hakki, Z. / Speciale, G. / Munoz-Munoz, J.L. / Day, A. / Pena, M.J. / Mclean, R. / Suits, M.D. / Boraston, A.B. / Atherly, T. / Ziemer, C.J. / Williams, S.J. / Davies, G.J. / Abbott, D.W. / Martens, E.C. / Gilbert, H.J.
History
DepositionAug 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Mar 4, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _software.name / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: MANNOSYL-6-PHOSPHATASE
B: MANNOSYL-6-PHOSPHATASE
C: MANNOSYL-6-PHOSPHATASE
D: MANNOSYL-6-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8939
Polymers133,7334
Non-polymers1595
Water14,772820
1
A: MANNOSYL-6-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4582
Polymers33,4331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANNOSYL-6-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5203
Polymers33,4331
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MANNOSYL-6-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4582
Polymers33,4331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MANNOSYL-6-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4582
Polymers33,4331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.440, 148.810, 71.450
Angle α, β, γ (deg.)90.00, 117.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MANNOSYL-6-PHOSPHATASE


Mass: 33433.344 Da / Num. of mol.: 4 / Fragment: RESIDUES 26-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
Gene: BT3783 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A183
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.14 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 8
Details: BT3783 CRYSTALS WERE OBTAINED BY MIXING EQUAL VOLUMES OF PURIFIED, RECOMBINANT BT3783 PROTEIN AT A CONCENTRATION OF 11.25 MG PER ML WITH MOTHER LIQUOR SOLUTION CONSISTING OF 15% (W/V) ...Details: BT3783 CRYSTALS WERE OBTAINED BY MIXING EQUAL VOLUMES OF PURIFIED, RECOMBINANT BT3783 PROTEIN AT A CONCENTRATION OF 11.25 MG PER ML WITH MOTHER LIQUOR SOLUTION CONSISTING OF 15% (W/V) POLYTHEYLENE GLYCOL 4,000, 5% MPD (V PER V), 3 MM D-MANNOSE, AND 200 MM MGCL2., pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97961
DetectorType: MARRESEARCH MX-300HE / Detector: CCD / Date: Mar 6, 2013
Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT)
RadiationMonochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 70728 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MPR

3mpr


Resolution: 2.1→39.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.206 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20495 3572 5.1 %RANDOM
Rwork0.1557 ---
obs0.1582 67122 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.46 Å2
2--1.3 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8627 0 8 820 9455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.92812028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17751072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50923.559472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.265151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8371556
X-RAY DIFFRACTIONr_chiral_restr0.1260.21222
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217004
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_it2.0911.9844276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0622.9515334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.262.2434623
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 294 -
Rwork0.203 4921 -
obs--100 %

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