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

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Basic information

Entry
Database: PDB / ID: 3zwk
TitleThe 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the metavanadate
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
VANADATE ION / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,5865
Polymers56,4392
Non-polymers1483
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-26.6 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.968, 71.364, 92.974
Angle α, β, γ (deg.)90.00, 95.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.80856, 0.00988, 0.58833), (0.00667, -0.99995, 0.00763), (0.58837, -0.00224, -0.80859)
Vector: -0.06381, 1.53611, 0.12104)

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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 / Plasmid: PKK223-3 / 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-VN3 / VANADATE ION / METAVANADATE


Mass: 98.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.12 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 10, 2010 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 30243 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 30.62 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.78
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.47 / % possible all: 96.5

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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: 2.099→46.276 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 1521 5 %
Rwork0.1555 --
obs0.1583 30231 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.464 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.371 Å20 Å21.9346 Å2
2--0.8176 Å20 Å2
3----2.1886 Å2
Refinement stepCycle: LAST / Resolution: 2.099→46.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 6 427 4313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074005
X-RAY DIFFRACTIONf_angle_d0.9795444
X-RAY DIFFRACTIONf_dihedral_angle_d13.4571523
X-RAY DIFFRACTIONf_chiral_restr0.062590
X-RAY DIFFRACTIONf_plane_restr0.005726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.17430.27551600.19792700X-RAY DIFFRACTION95
2.1743-2.26130.2561410.1772882X-RAY DIFFRACTION100
2.2613-2.36420.22591380.17052910X-RAY DIFFRACTION100
2.3642-2.48890.23641570.16022896X-RAY DIFFRACTION100
2.4889-2.64480.19991600.15352863X-RAY DIFFRACTION100
2.6448-2.8490.21331550.15162882X-RAY DIFFRACTION100
2.849-3.13560.20481410.15442887X-RAY DIFFRACTION100
3.1356-3.58920.21491580.15342886X-RAY DIFFRACTION99
3.5892-4.52140.18381600.13552893X-RAY DIFFRACTION99
4.5214-46.28720.20761510.16182911X-RAY DIFFRACTION98
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)
12.27290.5449-1.26310.2228-0.54793.9699-0.3358-0.2982-0.7748-0.24420.3113-0.3161.30950.17670.06230.45970.04650.03270.26010.02480.433637.824850.6257-17.5289
20.47110.5852-0.62290.9884-0.48751.7095-0.0143-0.1454-0.0214-0.0102-0.0774-0.16110.04980.13690.1080.06270.0236-0.01370.16780.02520.206433.982161.81561.5232
31.28080.8092-0.08070.9796-0.52412.33570.02030.38540.2734-0.14960.12120.31610.1863-0.6224-0.12770.17860.0345-0.01970.2834-0.00740.196118.963664.24471.8176
42.2242-0.36970.84761.9286-0.55431.94790.02760.2626-0.1363-0.31760.16810.21350.3117-0.13-0.16430.2018-0.0341-0.03570.1733-0.00870.185330.253858.8548-21.3608
51.4436-0.1995-0.38990.2358-0.61932.56520.20840.22620.73290.52690.05030.0505-1.3574-0.2399-0.1940.8982-0.05680.08630.20850.00780.334816.931860.066445.4135
60.51380.0029-0.37091.4819-0.01751.7826-0.0229-0.0669-0.06750.3440.0109-0.1214-0.01360.35670.01390.2032-0.0004-0.03690.2098-0.01160.159925.50248.061631.9657
70.69810.1596-0.75221.67220.12981.44250.02880.00470.1170.20940.11980.625-0.0075-0.5156-0.05350.15530.0230.01830.1918-0.02010.266412.757346.204221.4207
81.51290.7993-0.23411.23710.26980.6436-0.06560.18920.02790.57620.12190.48270.0167-0.4042-0.0750.5430.04420.09640.25390.05090.16899.018350.704245.6625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:35)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 36:146)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 147:175)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 176:252)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:29)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 30:142)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 143:176)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 177:252)

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