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- PDB-3zup: The 3-dimensional structure of MpgP from Thermus thermophilus HB2... -

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Basic information

Entry
Database: PDB / ID: 3zup
TitleThe 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the alpha-mannosylglycerate and orthophosphate reaction products.
ComponentsMANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
KeywordsHYDROLASE / HALOALKANOID ACID DEHALOGENASE-LIKE PHOSPHATASE / HAD-LIKE PHOSPHATASE
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate phosphatase activity / mannosylglycerate biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2M8 / PHOSPHATE ION / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsGoncalves, S. / Esteves, A.M. / Santos, H. / Borges, N. / Matias, P.M.
Citation
Journal: Biochemistry / Year: 2011
Title: The Three-Dimensional Structure of Mannosyl-3-Phosphoglycerate Phosphatase from Thermus Thermophilus Hb27: A New Member of the Haloalkanoic Acid Dehalogenase Superfamily.
Authors: Goncalves, S. / Esteves, A.M. / Santos, H. / Borges, N. / Matias, P.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and Preliminary X-Ray Analysis of Mannosyl-3-Phosphoglycerate Phosphatase from Thermus Thermophilus Hb27.
Authors: Goncalves, S. / Esteves, A.M. / Borges, N. / Santos, H. / Matias, P.M.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
B: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2148
Polymers56,4392
Non-polymers7756
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-44.1 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.368, 88.049, 146.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.82697, -0.49191, 0.27229), (-0.49021, -0.86799, -0.07928), (0.27534, -0.06792, -0.95894)
Vector: -0.35156, -0.36389, 0.23182)

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Components

#1: Protein MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE / / MPGP


Mass: 28219.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72K29, mannosyl-3-phosphoglycerate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-2M8 / (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid / 2-O-ALPHA-MANNOSYL-D-GLYCERATE / (2R)-3-hydroxy-2-(alpha-D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(mannosyloxy)propanoic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-O-ALPHA-MANNOSYL-D-GLYCERATE (MG9): MONOMER LIBRARY REFERENCE ENTRY 2M8

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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: 2.26 Å3/Da / Density % sol: 45.51 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REFERENCE IN REMARK 1, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 3, 2010 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. obs: 47907 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.29
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.67 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTY

3zty


Resolution: 1.804→42.161 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2342 5 %
Rwork0.1804 --
obs0.1829 46849 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.876 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6926 Å20 Å20 Å2
2---6.4708 Å20 Å2
3---3.7782 Å2
Refinement stepCycle: LAST / Resolution: 1.804→42.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 48 391 4351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074099
X-RAY DIFFRACTIONf_angle_d1.0325582
X-RAY DIFFRACTIONf_dihedral_angle_d13.0031578
X-RAY DIFFRACTIONf_chiral_restr0.065612
X-RAY DIFFRACTIONf_plane_restr0.005736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8041-1.86860.27712090.23013947X-RAY DIFFRACTION88
1.8686-1.94340.28242160.2154428X-RAY DIFFRACTION99
1.9434-2.03180.25282260.1914466X-RAY DIFFRACTION100
2.0318-2.1390.22372560.18144496X-RAY DIFFRACTION100
2.139-2.2730.22812380.17884476X-RAY DIFFRACTION100
2.273-2.44840.25512340.17944495X-RAY DIFFRACTION99
2.4484-2.69480.22062230.18414476X-RAY DIFFRACTION99
2.6948-3.08470.26242430.19014534X-RAY DIFFRACTION100
3.0847-3.88590.22342390.1774574X-RAY DIFFRACTION99
3.8859-42.17240.20252580.16644615X-RAY DIFFRACTION96
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)
10.8499-0.4313-0.14411.0755-0.16010.33510.04480.5575-0.1286-0.95270.18690.44430.6738-0.02780.00240.4563-0.0449-0.08940.2935-0.00110.2616-15.5164-45.502926.967
21.84230.51450.34571.83580.25921.0016-0.0230.07710.0990.00990.12370.3781-0.0711-0.1433-0.00020.09650.0076-0.0010.18220.01910.1845-17.1095-26.673434.2588
30.52550.3409-0.11332.5669-0.98421.2333-0.01410.07840.0394-0.17760.04990.00090.05290.05030.00010.0953-0.0005-0.00770.1549-0.01650.1243-7.3556-25.231428.378
42.0877-0.45010.74613.33130.56851.50370.03790.0239-0.20580.00160.0663-0.00070.20950.2802-0.00030.19740.0323-0.00860.2060.03260.19-7.7554-46.947535.9793
51.4717-0.14620.32960.9536-0.08290.39520.0379-0.51170.55840.371-0.1816-0.0029-0.2053-0.1623-0.00020.32120.03230.04520.3582-0.03210.28332.897213.29066.6986
61.75481.4474-0.92085.0748-2.11781.4751-0.05010.22930.079-0.97040.31220.74420.4168-0.192-0.00070.3712-0.0015-0.10270.19540.02670.1949-5.9021-4.72622.829
71.59661.0281-0.67822.0487-0.74280.6724-0.3471-0.4641-0.7298-0.99-0.6568-1.34210.69470.4643-0.02560.470.14420.25620.30770.1490.53966.6513-14.0186.0968
82.62570.7374-0.40112.9962-1.20061.09450.00580.0840.0567-0.8278-0.5354-0.88630.31320.6932-0.00060.3530.08210.09930.32520.13780.288810.79318.5111-1.4207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:29)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 30:107)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 108:189)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 190:252)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:29)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 30:143)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 144:177)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 178:252)

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