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- PDB-3zu6: The 3-dimensional structure of MpgP from Thermus thermophilus HB2... -

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Entry
Database: PDB / ID: 3zu6
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 / mannosyl-3-phosphoglycerate phosphatase activity / mannosylglycerate biosynthetic process / magnesium ion binding / cytosol
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: 1.9 Å
AuthorsGoncalves, S. / Borges, N. / Esteves, A.M. / Santos, H. / 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 14, 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: Atomic model / Derived calculations ...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 / 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: Data collection / Database references ...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
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)56,8265
Polymers56,4392
Non-polymers3873
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-26 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.930, 70.530, 92.630
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C9H16O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.3 Å3/Da / Density % sol: 46.8 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REMARK 1 REFERENCE ABOVE., pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.252
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: 1.252 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 114899 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.93 / % possible all: 85.7

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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: 1.9→20.852 Å / SU ML: 0.24 / σ(F): 0.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1950 5.1 %
Rwork0.1823 --
obs0.1851 38647 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.492 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2932 Å20 Å20.9552 Å2
2--0.3953 Å20 Å2
3----4.6885 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 24 323 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084005
X-RAY DIFFRACTIONf_angle_d1.1145446
X-RAY DIFFRACTIONf_dihedral_angle_d13.5321524
X-RAY DIFFRACTIONf_chiral_restr0.072593
X-RAY DIFFRACTIONf_plane_restr0.005722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.31661930.29343363X-RAY DIFFRACTION89
1.9679-2.04660.31842050.26243760X-RAY DIFFRACTION99
2.0466-2.13960.31232120.2363782X-RAY DIFFRACTION99
2.1396-2.25230.25372150.22093757X-RAY DIFFRACTION99
2.2523-2.39330.29161740.18933770X-RAY DIFFRACTION99
2.3933-2.57770.2521980.18153756X-RAY DIFFRACTION98
2.5777-2.83660.24652110.1773792X-RAY DIFFRACTION98
2.8366-3.24570.24412030.17633762X-RAY DIFFRACTION98
3.2457-4.08420.19691710.15343752X-RAY DIFFRACTION97
4.0842-20.85350.18871680.15563203X-RAY DIFFRACTION82
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)
10.87060.02720.80070.76930.31560.84520.34030.3011-1.5168-0.41950.13270.13671.32930.22840.00120.57890.0456-0.16780.3801-0.02530.765437.11652.1106-15.8123
21.37350.919-0.96481.5538-0.3993.30950.0059-0.2005-0.03630.1689-0.0963-0.14880.10160.17210.00010.08770.01930.0230.18660.07630.204634.944362.94022.0356
31.2989-0.00820.96840.7102-0.2842.01490.24740.1064-0.2634-0.50830.07360.38450.4872-1.0096-0.00210.22260.0053-0.05030.43530.0980.371318.474464.56012.5604
42.3784-2.20751.74592.9547-0.70693.02230.54320.2874-0.9396-0.45440.19460.70210.73910.0347-0.00040.3487-0.0521-0.22680.22360.04920.528629.516259.2838-20.1857
50.9356-0.11770.43710.63210.11680.42150.0956-0.1370.72470.358-0.1002-0.534-1.1377-0.1935-0.00020.67180.028-0.00340.3136-0.08020.419616.930959.166347.0148
61.35570.6607-0.49062.81570.07323.0263-0.0821-0.046-0.00240.28190.0098-0.143-0.22360.3798-0.00010.2140.0281-0.02960.2337-0.00740.18825.554948.492831.1132
71.6720.6075-0.0081.44071.24671.2764-0.07870.02410.0630.24370.15290.6324-0.3604-0.396-0.00010.24270.03050.01940.2075-0.00390.28812.643347.028321.5138
81.89360.18760.22462.20320.46352.03150.0422-0.1950.13260.3168-0.16440.30720.224-0.5648-0.00030.4562-0.01630.07650.3435-0.03970.20678.803750.461545.6462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:41)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 42:142)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 143:175)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 176:250)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:34)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 35:143)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 144:175)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 176:252)

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