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- PDB-3byc: Joint neutron and X-ray structure of diisopropyl fluorophosphatas... -

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Basic information

Entry
Database: PDB / ID: 3byc
TitleJoint neutron and X-ray structure of diisopropyl fluorophosphatase. Deuterium occupancies are 1-Q, where Q is occupancy of H
ComponentsDiisopropyl-fluorophosphatase
KeywordsHYDROLASE / beta-propeller / phosphotriesterase
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
DEUTERATED WATER / Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / existing x-ray model used / PDB id 2GVW / Resolution: 2.2 Å
AuthorsBlum, M.-M. / Mustyakimov, M. / Ruterjans, H. / Schoenborn, B.P. / Langan, P. / Chen, J.C.-H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2009
Title: Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
Authors: Blum, M.M. / Mustyakimov, M. / Ruterjans, H. / Kehe, K. / Schoenborn, B.P. / Langan, P. / Chen, J.C.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Data collection / Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2013
Polymers35,1211
Non-polymers802
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.441, 83.291, 87.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diisopropyl-fluorophosphatase / / E.C.3.1.8.2 / DFPase


Mass: 35120.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, diisopropyl-fluorophosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION2
NEUTRON DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2545.43
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion6.5PEG 4000, pH 6.5, vapor diffusion, temperature 298K
2982vapor diffusion, hanging drop6.5PEG 4000, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
13001
22982
Diffraction source
SourceTypeIDWavelength (Å)
10.6, 7.0
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDate
BNL1TOF AREA DETECTORJan 1, 2007
MAR scanner 345 mm plate2IMAGE PLATEMay 25, 2004
Radiation
TypeIDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
neutron1WAVELENGTH-RESOLVED LAUELneutron1
x-ray2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
271
31.54181
ReflectionResolution: 1.85→38.91 Å / Num. all: 13656 / Num. obs: 12068 / % possible obs: 43.3 % / Observed criterion σ(F): 2.5 / Biso Wilson estimate: 4.1 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 44 / Limit k min: 0 / Limit l max: 47 / Limit l min: 0 / Observed criterion F max: 2011245.43 / Observed criterion F min: 107.5

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Processing

SoftwareName: nCNS / Version: 1.0.0 / Classification: refinement / Contact author: Marat Mustyakimov / Contact author email: marat[at]lanl.gov / Date: 2008 / Language: Fortran / URL: http://mnc.lanl.gov / Type: package
Refinement

Biso max: 89.84 Å2 / Biso mean: 25.9 Å2 / Biso min: 2 Å2 / Rfactor Rfree error: 0.013 / Num. reflection Rfree: 564 / Num. reflection all: 13629 / Num. reflection obs: 12042 / % reflection Rfree: 4.7 % / % reflection obs: 72 % / Occupancy max: 1 / Occupancy min: 0 / R Free selection details: random / Data cutoff high absF: 2011245.43 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber / Solvent model: CNS bulk solvent model used / Bsol: 63.8081 Å2 / ksol: 0.713641 e/Å3 / Resolution: 2.2→19.54 Å

Method to determine structureRefine-IDRfactor RfreeRfactor RworkDiffraction-ID
existing x-ray model usedNEUTRON DIFFRACTION0.3150.2641
PDB id 2GVWX-RAY DIFFRACTION0.2520.2332
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 2 246 2699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg15.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.30.4595.10.35511050.0522061116456.5
2.3-2.420.327524.40.32111310.0452050118357.7
2.42-2.570.3976450.34312090.052070127361.5
2.57-2.770.417574.30.33712720.0552039132965.2
2.77-3.050.34654.50.29313880.0422077145370
3.05-3.490.3210060.27915530.0322092165379
3.49-4.390.2527540.2117870.0292121186287.8
4.39-19.540.267924.30.20520330.0282213212596
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein-allhdg_hd.paramprotein-allhdg_hd.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3dod.paramdod.top

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