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- PDB-3zx5: The 3-dimensional structure of MpgP from Thermus thermophilus HB2... -

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Basic information

Entry
Database: PDB / ID: 3zx5
TitleThe 3-dimensional structure of MpgP from Thermus thermophilus HB27, covalently bound to vanadate and in complex with alpha- mannosylglycerate and magnesium
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 / oxido(dioxo)vanadium / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionAug 7, 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)57,2218
Polymers56,4392
Non-polymers7836
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-25.6 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.948, 71.263, 91.217
Angle α, β, γ (deg.)90.00, 95.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.81598, -0.01791, 0.5778), (-0.03391, -0.99928, 0.01691), (0.57708, -0.03339, -0.81601)
Vector: -2.87725, 110.92876, 13.6741)

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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-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO3
#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


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETAVANADATE (VN4): METAVANADATE IS COVALENTLY LINKED TO ASP6 OD OXYGEN

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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: 2.37 Å3/Da / Density % sol: 48.03 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REFERENCE 1 IN REMARK 1., pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.81→30 Å / Num. obs: 46178 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 27.02 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.99
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.92 / % possible all: 98.8

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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: 1.81→28.772 Å / SU ML: 0.25 / σ(F): 1.05 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 2340 5.1 %
Rwork0.168 --
obs0.1702 46174 99.37 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.098 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3381 Å20 Å20.4278 Å2
2--2.3878 Å20 Å2
3----6.7259 Å2
Refinement stepCycle: LAST / Resolution: 1.81→28.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 46 391 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074043
X-RAY DIFFRACTIONf_angle_d1.0725503
X-RAY DIFFRACTIONf_dihedral_angle_d12.5441543
X-RAY DIFFRACTIONf_chiral_restr0.07605
X-RAY DIFFRACTIONf_plane_restr0.005727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8102-1.87490.33352320.28024274X-RAY DIFFRACTION98
1.8749-1.94990.26192370.22664373X-RAY DIFFRACTION99
1.9499-2.03860.25982330.1854355X-RAY DIFFRACTION99
2.0386-2.14610.2082490.16444386X-RAY DIFFRACTION100
2.1461-2.28050.23082190.1554391X-RAY DIFFRACTION100
2.2805-2.45650.21242200.16034376X-RAY DIFFRACTION99
2.4565-2.70350.23272530.16644373X-RAY DIFFRACTION100
2.7035-3.09430.20082230.1734416X-RAY DIFFRACTION99
3.0943-3.8970.19612410.15844401X-RAY DIFFRACTION99
3.897-28.77530.19382330.1584489X-RAY DIFFRACTION99
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)
10.52540.15480.15560.29930.11481.00580.0484-0.1134-0.6941-0.01640.0079-0.16391.57630.3920.00520.5890.1026-0.00780.25790.01470.355137.085851.5384-15.8297
21.43370.1796-0.16511.9578-0.64673.19210.0167-0.24590.00660.0859-0.1113-0.05820.21580.1577-0.00020.1215-0.0213-00.22570.05470.198634.427662.04092.251
31.1138-0.29221.18121.03050.10611.49230.0436-0.02460.1116-0.00020.07840.17170.0061-0.568-00.1791-0.0193-0.00330.28470.06530.23726.168366.5679-4.8028
40.8499-0.30290.7831.17150.49871.29190.14650.1962-0.2926-0.3340.10050.33220.7276-0.2694-0.00010.4125-0.0637-0.09530.30790.04780.337927.439856.1951-20.6103
50.8691-0.254-0.07480.51520.3860.43320.0738-0.16680.36790.5467-0.0852-0.1835-0.72430.3060.00010.4635-0.064-0.05150.2124-0.04760.279417.327858.145646.531
60.37130.393-0.22550.6858-0.02570.50550.0725-0.0247-0.07650.4659-0.1182-0.39050.00360.46850.00050.2969-0.0288-0.06650.240.03960.254527.191146.060841.445
71.32080.3425-0.14631.49850.26262.7581-0.04770.14130.01930.0447-0.0066-0.00110.02930.08030.00010.1373-0.0228-0.01510.1510.01940.194118.813346.928928.1372
80.89870.08580.07080.6344-0.36540.3234-0.149-0.01640.33620.17850.01190.772-0.1462-0.72310.00060.3321-0.03860.04270.2575-0.06230.33555.09356.032744.5674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:38)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 39:146)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 147:191)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 192:250)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:36)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 37:80)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 81:209)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 210:250)

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