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- PDB-1pjx: 0.85 ANGSTROM STRUCTURE OF SQUID GANGLION DFPASE -

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Basic information

Entry
Database: PDB / ID: 1pjx
Title0.85 ANGSTROM STRUCTURE OF SQUID GANGLION DFPASE
ComponentsDIISOPROPYLFLUOROPHOSPHATASE
KeywordsHYDROLASE / PHOSPHOTRIESTERASE (PTE) / NITROGEN-CALCIUM COORDINATION / BETA-PROPELLER / BOND-LENGTH AND BOND-ANGLE RESTRAINTS / TORSION ANGLES / ROTAMER CLASSIFICATION
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
1,2-DIMETHOXYETHANE / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / 2-METHOXYETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsKoepke, J. / Rueterjans, H. / Luecke, C. / Fritzsch, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.
Authors: Koepke, J. / Scharff, E.I. / Lucke, C. / Ruterjans, H. / Fritzsch, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-ray Crystallographic Analysis of DFPase from Loligo Vulgaris
Authors: Scharff, E.I. / Luecke, C. / Fritzsch, G. / Koepke, J. / Hartleib, J. / Dierl, S. / Rueterjans, H.
#2: Journal: Structure / Year: 2001
Title: Crystal Structure of Diisopropylfluorophosphatase from Loligo Vulgaris
Authors: Scharff, E.I. / Koepke, J. / Fritzsch, G. / Luecke, C. / Rueterjans, H.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Atomic Resolution Crystal Structure of Squid Ganglion DFPase
Authors: Koepke, J. / Scharff, E.I. / Luecke, C. / Rueterjans, H. / Fritzsch, G.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.pdbx_leaving_atom_flag / _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: DIISOPROPYLFLUOROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,35525
Polymers35,1211
Non-polymers2,23524
Water8,629479
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.114, 81.849, 86.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DIISOPROPYLFLUOROPHOSPHATASE / DFPASE


Mass: 35120.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Organ: HEAD GANGLION / Plasmid: PKKHISND / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7SIG4, EC: 3.1.8.2

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Non-polymers , 10 types, 503 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 479 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 43.34 %
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 2000 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 0.835→10 Å / Num. obs: 264548 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.7
Reflection shellResolution: 0.835→0.85 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.8 / % possible all: 77.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1A

1e1a


Resolution: 0.85→10 Å / Num. parameters: 29658 / Num. restraintsaints: 30675 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.04
RfactorNum. reflection% reflectionSelection details
Rfree0.1284 2497 1 %RANDOM
all0.1109 240480 --
obs0.1206 240480 90.8 %-
Refine analyzeNum. disordered residues: 63 / Occupancy sum hydrogen: 2047.3 / Occupancy sum non hydrogen: 2921.39
Refinement stepCycle: LAST / Resolution: 0.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 142 479 3080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.061
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0336
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.208
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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