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

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Basic information

Entry
Database: PDB / ID: 3zwd
TitleThe 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the alpha-mannosylglycerate.
ComponentsMANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
KeywordsHYDROLASE / HALOALKANOID ACID DEHALOGENASE-LIKE PHOSPHATASE / HAD-LIKE PHOSPHATASE / CRYSTALLOGRAPHIC SNAPSHOT
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 / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.917 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 28, 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)56,9995
Polymers56,4392
Non-polymers5613
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-17 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.868, 70.239, 91.783
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.81363, 0.04119, 0.57992), (-0.00056, -0.99743, 0.07162), (0.58138, -0.05859, -0.81152)
Vector: -6.08105, 109.40703, 15.61256)

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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: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details2-O-ALPHA-MANNOSYL-D-GLYCERATE (DMG): 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: 2.34 Å3/Da / Density % sol: 47.48 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REFERENCE 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: 1.91→60 Å / Num. obs: 37993 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.64 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.28
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.74 / % possible all: 92.9

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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: 1.917→28.769 Å / SU ML: 0.25 / σ(F): 1.69 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1911 5.1 %
Rwork0.161 --
obs0.1637 37742 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.107 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3651 Å2-0 Å22.8704 Å2
2--3.0928 Å20 Å2
3----8.4579 Å2
Refinement stepCycle: LAST / Resolution: 1.917→28.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 37 435 4351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074010
X-RAY DIFFRACTIONf_angle_d0.9865452
X-RAY DIFFRACTIONf_dihedral_angle_d13.2741525
X-RAY DIFFRACTIONf_chiral_restr0.063599
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9173-1.98580.28981670.22033271X-RAY DIFFRACTION89
1.9858-2.06530.24351970.18823622X-RAY DIFFRACTION99
2.0653-2.15930.21842210.16263615X-RAY DIFFRACTION100
2.1593-2.27310.22441740.15833673X-RAY DIFFRACTION100
2.2731-2.41540.19361860.15073665X-RAY DIFFRACTION100
2.4154-2.60180.22822010.15543636X-RAY DIFFRACTION99
2.6018-2.86340.23311970.16443622X-RAY DIFFRACTION99
2.8634-3.27720.19181760.15953571X-RAY DIFFRACTION97
3.2772-4.1270.21062040.15213586X-RAY DIFFRACTION97
4.127-28.77180.20631880.16143570X-RAY DIFFRACTION95
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)
11.0282-0.3971-0.02950.42690.53772.19530.0227-0.3848-1.11290.2684-0.02530.42521.4449-0.10590.00570.55110.0328-0.01860.27740.04420.543635.815549.6019-15.2028
22.36080.3236-0.12791.7977-0.04612.363-0.0483-0.2473-0.09880.0192-0.0703-0.0811-0.05790.3858-0.00020.0949-0.0059-0.00130.16810.03850.200937.62665.1906-3.097
31.6224-0.0567-0.07442.5926-1.1785.1007-0.041-0.0403-0.0681-0.05810.0330.19340.3092-0.53290.00030.1182-0.043-0.00070.2180.02120.220525.075659.41885.1003
43.0433-0.57591.47853.20930.35383.21530.1360.1916-0.5186-0.32530.15860.36510.5397-0.13790.00040.2691-0.0396-0.06360.19450.03760.29329.419358.0722-20.2761
51.3781-0.077-0.42430.503-0.7062.12610.069-0.20560.32860.2563-0.0467-0.0888-0.3940.1932-00.3708-0.0258-0.01930.2384-0.04470.215920.356654.208243.4659
60.64920.2801-0.39142.0516-0.23472.9761-0.042-0.0214-0.01650.12440.0147-0.1502-0.0190.4154-0.00020.13830.0008-0.03290.2118-0.00130.196626.019346.957727.8901
72.24810.3976-0.29331.17291.30621.8971-0.0550.12450.15040.09950.07790.4342-0.1076-0.327-00.1784-0.0114-0.01270.21170.00920.25312.822846.388521.3915
81.76450.1451-0.46551.75380.26742.3279-0.0821-0.23710.09810.33480.04660.27820.0836-0.3927-0.00010.3672-0.01110.04160.2917-0.02990.19678.776649.625945.3848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:29)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 30:104)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 105:177)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 178:251)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:64)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 65:143)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 144:175)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 176:252)

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