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Entry
Database: PDB / ID: 3ks6
TitleCrystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 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 / DI(HYDROXYETHYL)ETHER / Unknown ligand / Glycerophosphoryl diester phosphodiesterase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.80 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 6, 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 / _struct_ncs_dom_lim.end_label_seq_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
C: Glycerophosphoryl diester phosphodiesterase
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,81421
Polymers109,1154
Non-polymers69917
Water23,8161322
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5637
Polymers27,2791
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4215
Polymers27,2791
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3624
Polymers27,2791
Non-polymers833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4685
Polymers27,2791
Non-polymers1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.427, 99.797, 134.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 1 - 246 / Label seq-ID: 2 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycerophosphoryl diester phosphodiesterase


Mass: 27278.688 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 1339 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 35.0000% 2-propanol, 0.1M Acetate pH 4.5, 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: 0.91837,0.97951,0.97870
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 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
20.979511
30.97871
ReflectionResolution: 1.8→29.828 Å / Num. obs: 104654 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.364 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.854.10.66223161976850.662100
1.85-1.94.10.5151.53067974490.515100
1.9-1.954.10.4131.82987272650.413100
1.95-2.014.10.3222.42897570180.322100
2.01-2.084.10.25232842968890.252100
2.08-2.154.10.2173.52733766170.217100
2.15-2.234.10.1764.32652064200.176100
2.23-2.324.10.1524.82547261600.152100
2.32-2.434.10.1285.82446959160.128100
2.43-2.554.10.1086.82343656720.108100
2.55-2.684.10.09182240754090.091100
2.68-2.854.10.0838.42111451140.083100
2.85-3.044.10.079.61988648210.07100
3.04-3.294.10.05910.91862145130.059100
3.29-3.64.10.04713.81711641620.047100
3.6-4.024.10.04115.21540037560.041100
4.02-4.654.10.04214.81380733900.042100
4.65-5.6940.04513.51145828510.045100
5.69-8.053.90.05212882922570.05299.9
8.05-29.833.70.04213.9472012900.04297.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.828 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.647 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114
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 SELENOMETHIONINE 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 SELENOMETHIONINE 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) AND CHLORIDE IONS(CL) FROM CRYSTALLIZATION AND POLYETHYLENE GLYCOL(PEG) MOLECULES FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 4.MG ION AND ONE UNKNOWN LIGAND ARE MODELED IN THE CONSERVED ACTIVE SITE OF EACH SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5227 5 %RANDOM
Rwork0.166 ---
obs0.168 104578 99.96 %-
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: 81 Å2 / Biso mean: 26.606 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 58 1322 9129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227976
X-RAY DIFFRACTIONr_bond_other_d0.0020.025173
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.95310895
X-RAY DIFFRACTIONr_angle_other_deg1.05312662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.74451055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0822.903310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.919151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5061554
X-RAY DIFFRACTIONr_chiral_restr0.0860.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029083
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021615
X-RAY DIFFRACTIONr_nbd_refined0.2040.31751
X-RAY DIFFRACTIONr_nbd_other0.1850.35584
X-RAY DIFFRACTIONr_nbtor_refined0.1710.53994
X-RAY DIFFRACTIONr_nbtor_other0.0880.53818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.51621
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.360
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.557
X-RAY DIFFRACTIONr_mcbond_it2.03935350
X-RAY DIFFRACTIONr_mcbond_other0.57432082
X-RAY DIFFRACTIONr_mcangle_it2.6858309
X-RAY DIFFRACTIONr_scbond_it4.46483017
X-RAY DIFFRACTIONr_scangle_it5.682112586
Refine LS restraints NCS

Ens-ID: 1 / Number: 2838 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.315
2BLOOSE POSITIONAL0.345
3CLOOSE POSITIONAL0.255
4DLOOSE POSITIONAL0.315
1ALOOSE THERMAL2.9210
2BLOOSE THERMAL3.7910
3CLOOSE THERMAL2.610
4DLOOSE THERMAL3.8710
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 366 -
Rwork0.231 7311 -
all-7677 -
obs--100 %

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