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- PDB-1zcc: Crystal structure of glycerophosphodiester phosphodiesterase from... -

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Basic information

Entry
Database: PDB / ID: 1zcc
TitleCrystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58
Componentsglycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / NYSGXRC / T2047 / Glycerophosphodiester phosphodiesterase / Agrobacterium tumefaciens str. C58 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research 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
ACETATE ION / Glycerophosphodiester phosphodiesterase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKrishnamurthy, N.R. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.
Authors: Rao, K.N. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerophosphodiester phosphodiesterase
B: glycerophosphodiester phosphodiesterase
C: glycerophosphodiester phosphodiesterase
D: glycerophosphodiester phosphodiesterase
E: glycerophosphodiester phosphodiesterase
F: glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,09118
Polymers164,1606
Non-polymers93112
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-155 kcal/mol
Surface area46670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.560, 140.220, 88.600
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly within the asymmetric unit is a hexamer formed by dimer of trimers.

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Components

#1: Protein
glycerophosphodiester phosphodiesterase


Mass: 27360.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U887, UniProt: A9CG82*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.93 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium sulfate, PEG8K, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X12C20.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 5, 2005Mirrors
BRANDEIS - B42CCDNov 22, 2004Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9791
ReflectionResolution: 2.4→50 Å / Num. all: 75568 / Num. obs: 75568 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.104 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.4 % / Num. unique all: 7418 / Rsym value: 0.43 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 626023.61 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The residues listed in remark 470 were modelled as ALA due to the lack of electron density. The residues listed in remark 465 were not modelled due to the lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1264 2 %RANDOM
Rwork0.244 ---
obs0.244 62460 94.2 %-
all-62460 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2296 Å2 / ksol: 0.335671 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1--14.08 Å20 Å23.35 Å2
2---5.98 Å20 Å2
3---20.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10656 0 54 276 10986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 179 1.9 %
Rwork0.336 9336 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4so4_xplor_par.txtso4_xplor_top.txt
X-RAY DIFFRACTION5act_xplor_par.txtact_xplor_top.txt

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