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- PDB-3ks5: Crystal structure of Putative glycerophosphoryl diester phosphodi... -

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Basic information

Entry
Database: PDB / ID: 3ks5
TitleCrystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution
ComponentsGlycerophosphoryl diester phosphodiesterase
KeywordsHYDROLASE / Putative glycerophosphoryl diester phosphodiesterase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Plasmid
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding
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
ACETATE ION / : / Glycerophosphoryl diester phosphodiesterase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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.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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerophosphoryl diester phosphodiesterase
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70321
Polymers54,5572
Non-polymers1,14619
Water6,395355
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,88111
Polymers27,2791
Non-polymers60210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,82210
Polymers27,2791
Non-polymers5439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.153, 84.153, 214.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ACT / End label comp-ID: ACT / Refine code: 4 / Auth seq-ID: 7 - 251 / Label seq-ID: 8

Dom-IDAuth asym-IDLabel asym-ID
1AA - D
2BB - N

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Components

#1: Protein Glycerophosphoryl diester phosphodiesterase


Mass: 27278.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Strain: C58 / ATCC 33970 / Gene: 17743486, AGR_pAT_81, Atu5061, glpQ / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9CLR1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97855,0.97783
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978551
30.977831
ReflectionResolution: 2.05→30.069 Å / Num. obs: 49371 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 34.435 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.120.9711.429754849695.9
2.12-2.210.7171.935271981499.8
2.21-2.310.5412.533474918599.8
2.31-2.430.393.533696913099.9
2.43-2.580.267534273914899.9
2.58-2.780.1896.935483933199.8
2.78-3.060.11810.735740927399.8
3.06-3.50.06618.235912927499.7
3.5-4.40.0428.735757923099.8
4.4-30.0690.02935.936338935299.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.05→30.069 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.753 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIOFENE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIOFENE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ACETATE IONS(ACT) FROM CRYSTALLIZATION AND ETHYLENE GLYCOL(EDO) FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 4.ONE FE ION IS MODELED IN EACH CONSERVED ACTIVE SITE. THE PRESENCE OF FE IONS ARE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2492 5.1 %RANDOM
Rwork0.212 ---
obs0.214 49285 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.82 Å2 / Biso mean: 46.781 Å2 / Biso min: 22.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 70 355 4249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223971
X-RAY DIFFRACTIONr_bond_other_d0.0030.022579
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9545396
X-RAY DIFFRACTIONr_angle_other_deg1.18436308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.21123.158152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94115624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02787
X-RAY DIFFRACTIONr_nbd_refined0.1870.3849
X-RAY DIFFRACTIONr_nbd_other0.1620.32711
X-RAY DIFFRACTIONr_nbtor_refined0.1660.51920
X-RAY DIFFRACTIONr_nbtor_other0.0840.51823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5490
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.526
X-RAY DIFFRACTIONr_mcbond_it2.07332840
X-RAY DIFFRACTIONr_mcbond_other1.02231030
X-RAY DIFFRACTIONr_mcangle_it2.79154097
X-RAY DIFFRACTIONr_scbond_it4.57981526
X-RAY DIFFRACTIONr_scangle_it5.753111299
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2951 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.340.5
MEDIUM THERMAL2.312
LS refinement shellResolution: 2.049→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 195 -
Rwork0.289 3293 -
all-3488 -
obs--97.21 %

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