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- PDB-3ztw: The 3-dimensional structure of apo-MpgP, the mannosyl-3- phosphog... -

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Basic information

Entry
Database: PDB / ID: 3ztw
TitleThe 3-dimensional structure of apo-MpgP, the mannosyl-3- phosphoglycerate phosphatase from Thermus thermophilus HB27 in its apo-form
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 / 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
PHOSPHATE ION / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 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 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 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 / 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 / _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-3-PHOSPHOGLYCERATE PHOSPHATASE
B: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6294
Polymers56,4392
Non-polymers1902
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-21.9 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.520, 70.686, 95.422
Angle α, β, γ (deg.)90.00, 92.95, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.44 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE REMARK 1 REFERENCE, 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 QUANTUM 315r / Detector: CCD / Date: Mar 14, 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: 1.9→50 Å / Num. obs: 40742 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 29.45 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 88.6

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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: 1.898→39.51 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 2073 5.1 %
Rwork0.173 --
obs0.1757 40720 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.34 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.823 Å20 Å24.1558 Å2
2---0.5378 Å20 Å2
3----1.2852 Å2
Refinement stepCycle: LAST / Resolution: 1.898→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 10 439 4290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073974
X-RAY DIFFRACTIONf_angle_d0.9655405
X-RAY DIFFRACTIONf_dihedral_angle_d12.3841508
X-RAY DIFFRACTIONf_chiral_restr0.06586
X-RAY DIFFRACTIONf_plane_restr0.005718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8982-1.96610.30311750.24163298X-RAY DIFFRACTION84
1.9661-2.04480.26462170.20453802X-RAY DIFFRACTION98
2.0448-2.13790.26232150.1923902X-RAY DIFFRACTION100
2.1379-2.25060.23992090.17293951X-RAY DIFFRACTION100
2.2506-2.39160.24961940.16553928X-RAY DIFFRACTION100
2.3916-2.57620.21282190.16993917X-RAY DIFFRACTION100
2.5762-2.83540.23342200.17223937X-RAY DIFFRACTION100
2.8354-3.24550.24341940.16973958X-RAY DIFFRACTION100
3.2455-4.08830.18292170.15773945X-RAY DIFFRACTION100
4.0883-39.51830.2082130.15264009X-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)
11.24980.2068-0.39340.05470.21782.92880.0168-0.3979-1.19820.42130.1246-0.26731.54910.07960.00680.53940.0232-0.04070.31970.0080.541636.893849.5074-18.2462
21.36540.6224-0.91041.4308-1.09632.2113-0.0069-0.08630.03060.0554-0.0594-0.09410.00910.178-00.10930.0185-0.02920.19710.03360.205934.842761.0708-0.0224
30.8911-0.02570.47660.1538-0.13811.140.06460.24230.0153-0.0150.16360.30050.0473-0.7341-0.00020.15770.02360.00450.39240.05610.302717.979762.61122.1102
42.2638-0.2691.33321.7290.13092.5516-0.09460.3458-0.4069-0.32920.16770.17250.3270.100900.2491-0.0233-0.01210.25740.0140.261729.937158.3379-22.2433
50.5009-0.4266-0.10160.33810.13390.20040.0891-0.05020.67670.4321-0.2493-0.031-0.8136-0.1776-0.00220.7152-0.02830.03690.2884-0.0850.322219.932657.06750.1608
60.48690.1749-0.38832.0415-0.2172.60630.01580.0328-0.05970.2544-0.1023-0.1923-0.02240.2997-0.00030.1619-0.0087-0.03460.19310.00060.188226.350946.523331.0955
70.80780.4653-0.07242.0382-0.13052.84430.04780.17050.12820.2058-0.07560.3447-0.1333-0.20920.00010.1731-0.00250.03080.1949-0.01380.228518.025346.914126.8643
81.756-0.2018-0.61462.09870.60121.1355-0.09650.0081-0.05640.8731-0.37650.99470.0186-0.3573-0.00010.5073-0.07850.18110.2406-0.14160.387810.389952.596449.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:32)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 33:141)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 142:175)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 176:252)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:34)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 35:125)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 126:187)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 188:253)

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