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- PDB-1o1z: Crystal structure of glycerophosphodiester phosphodiesterase (GDP... -

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Entry
Database: PDB / ID: 1o1z
TitleCrystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution
Componentsglycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / TM1621 / GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid metabolic process
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GP-PDE domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.
Authors: Santelli, E. / Schwarzenbacher, R. / McMullan, D. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / ...Authors: Santelli, E. / Schwarzenbacher, R. / McMullan, D. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Rezezadeh, F. / Robb, A. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1932
Polymers27,1701
Non-polymers231
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.410, 41.790, 51.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein glycerophosphodiester phosphodiesterase / GDPD


Mass: 27170.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1621 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X1V6, glycerophosphodiester phosphodiesterase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.22 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 277 K / pH: 9.6
Details: 40% (v/v) PEG-600, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 9.60
Crystal grow
*PLUS
pH: 9.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
420 mg/mlprotein1drop
540 %PEG6001reservoir
60.1 MCHES1reservoirpH9.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98011, 0.97938, 0.97918, 0.95671
DetectorType: APS-1 / Detector: CCD / Date: Oct 26, 2002
Details: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
20.979381
30.979181
40.956711
ReflectionResolution: 1.6→50 Å / Num. obs: 38012 / % possible obs: 100 % / Redundancy: 6.71 % / Rsym value: 0.05 / Net I/σ(I): 62.01
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.51 % / Mean I/σ(I) obs: 10.06 / Rsym value: 0.196 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Observed criterion σ(F): 0 / Num. measured all: 255060 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building
SOLVEphasing
ARP/wARPmodel building
REFMAC5.1.955refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→48.18 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.507 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: WEAK CONTINUOUS DIFFERENCE DENSITY AT THE N-TERMINUS WAS MODELLED AS HIS-TAG RESIDUES, BUT AT HALF OCCUPANCY.THE CONTINUED PRESENCE OF SPURIOUS DIFFERENCE DENSITY IMPLIES THAT THIS STILL IS ...Details: WEAK CONTINUOUS DIFFERENCE DENSITY AT THE N-TERMINUS WAS MODELLED AS HIS-TAG RESIDUES, BUT AT HALF OCCUPANCY.THE CONTINUED PRESENCE OF SPURIOUS DIFFERENCE DENSITY IMPLIES THAT THIS STILL IS AN INCOMPLETE DESCRIPTION OF THE N-TERMINUS. XFIT/CCP4/TLS WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1926 5.1 %RANDOM
Rwork0.139 ---
obs0.141 36027 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 1 422 2254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211909
X-RAY DIFFRACTIONr_bond_other_d0.0020.021796
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9692571
X-RAY DIFFRACTIONr_angle_other_deg0.88234177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0524.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0461515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined0.2110.2383
X-RAY DIFFRACTIONr_nbd_other0.2380.22207
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.21177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3360.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7941129
X-RAY DIFFRACTIONr_mcangle_it3.05461841
X-RAY DIFFRACTIONr_scbond_it4.41110780
X-RAY DIFFRACTIONr_scangle_it6.90513730
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.218 137
Rwork0.165 2413
Refinement TLS params.Method: refined / Origin x: 20.0943 Å / Origin y: 8.3707 Å / Origin z: 2.9538 Å
111213212223313233
T0.0002 Å20.0026 Å20.0081 Å2--0.0243 Å20.0158 Å2--0.0241 Å2
L0.8771 °20.1355 °2-0.1374 °2-0.5342 °20.2144 °2--1.2711 °2
S-0.0123 Å °0.0176 Å °0.0003 Å °-0.0051 Å °-0.0029 Å °0.0649 Å °-0.0301 Å °-0.098 Å °0.0152 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-3 - 2229 - 234
2X-RAY DIFFRACTION1AB602
3X-RAY DIFFRACTION1AC603 - 958
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection all: 37953 / % reflection Rfree: 5.1 % / Rfactor Rfree: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.41

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