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- PDB-3zty: The 3-dimensional structure of the gadolinium derivative of MpgP,... -

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Basic information

Entry
Database: PDB / ID: 3zty
TitleThe 3-dimensional structure of the gadolinium derivative of MpgP, the mannosyl-3-phosphoglycerate phosphatase from Thermus thermophilus HB27
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
GADOLINIUM ATOM / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 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 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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)57,45310
Polymers56,4392
Non-polymers1,0148
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-98.9 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.692, 70.835, 92.735
Angle α, β, γ (deg.)90.00, 95.04, 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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGADOLINIUM (III) (GD): FROM GDCL3

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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: 2.31 Å3/Da / Density % sol: 46.7 % / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 21, 2010
RadiationMonochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→39.5 Å / Num. obs: 17882 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.7 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SAINTdata reduction
SADABSdata scaling
SHELXCDEphasing
autoSHARPphasing
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→37.561 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 908 5.1 %
Rwork0.1953 --
obs0.1983 17834 99.82 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.197 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2694 Å20 Å20.4107 Å2
2---2.1267 Å20 Å2
3----2.1426 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 8 146 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083984
X-RAY DIFFRACTIONf_angle_d1.125420
X-RAY DIFFRACTIONf_dihedral_angle_d15.6861514
X-RAY DIFFRACTIONf_chiral_restr0.066588
X-RAY DIFFRACTIONf_plane_restr0.005724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.65670.28281400.22852817X-RAY DIFFRACTION100
2.6567-2.86180.30661540.22362798X-RAY DIFFRACTION100
2.8618-3.14960.27711400.21752823X-RAY DIFFRACTION100
3.1496-3.60510.26061470.19532830X-RAY DIFFRACTION100
3.6051-4.54070.24771670.17322807X-RAY DIFFRACTION100
4.5407-37.56570.21271600.18322851X-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)
11.0265-0.1040.65730.71520.39740.5679-0.0684-0.3256-0.7378-0.4930.2262-0.20171.51320.4460.00060.71980.1355-0.07670.36610.01990.557535.897949.7695-16.4032
21.54290.5593-1.3432.184-1.22463.69720.0259-0.15460.0167-0.0073-0.1395-0.19040.05520.1172-0.00020.07740.0074-0.03360.23670.01460.220635.492561.5956-0.2611
32.2082-1.7750.21271.4877-0.35142.59850.18880.3159-0.3766-0.21940.06760.5640.0166-0.68820.00040.15820.0453-0.03160.39310.03250.367621.528762.5762.5746
42.5903-1.58691.78513.4921-1.0192.78260.10340.1917-0.6806-0.81810.15340.47590.6261-0.3295-0.00010.3928-0.1016-0.08510.29090.00750.425329.447459.0043-20.7725
51.3903-0.58860.17160.79040.44420.4224-0.11860.13330.48950.7139-0.0646-0.2135-1.40230.254-0.00040.7691-0.11220.00880.3617-0.0210.423716.721259.848545.572
61.03541.35840.19451.89140.17521.48630.149-0.3866-0.17330.7884-0.0349-0.65630.15940.57740.00010.54870.0251-0.0850.37710.03910.288426.396146.904443.0672
71.74131.89280.18763.78390.57773.73590.03220.00890.1292-0.01990.01180.2104-0.15270.0402-0.00010.14340.02250.01260.2191-0.01940.214920.36848.205721.6996
83.13030.6980.01912.3905-0.35552.2848-0.1169-0.05680.16360.55620.1040.62920.1207-0.61610.00020.5707-0.0430.08710.4045-0.06620.28938.875150.99945.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:29)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 30:132)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 133:175)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 176:251)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:29)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 30:83)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 84:176)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 177:251)

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