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- PDB-2paj: Crystal structure of an amidohydrolase from an environmental samp... -

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Basic information

Entry
Database: PDB / ID: 2paj
TitleCrystal structure of an amidohydrolase from an environmental sample of Sargasso sea
Componentsputative cytosine/guanine deaminase
KeywordsHYDROLASE / NYSGXRC / 9339a / PSI-II / amidohydrolase / Sargasso sea / environmental sample / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Roll / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Roll / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2010
Title: Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase.
Authors: Hall, R.S. / Agarwal, R. / Hitchcock, D. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / Raushel, F.M.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE ANALYSIS OF PROTEIN INTERFACES PREDICTS THAT THE BIOLOGICAL UNIT COULD HAVE THE FOLLOWING DIMERIC ASSEMBLY: CHAIN A (X,Y,Z (1_555); Y,X,-Z (4_555)).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative cytosine/guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0922
Polymers53,0271
Non-polymers651
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: putative cytosine/guanine deaminase
hetero molecules

A: putative cytosine/guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1854
Polymers106,0542
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4100 Å2
ΔGint-96 kcal/mol
Surface area30380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.872, 88.872, 161.867
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein putative cytosine/guanine deaminase


Mass: 53027.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5, 12% PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2007 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 19968 / Num. obs: 19968 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Redundancy: 19 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1 / Num. unique all: 1297 / % possible all: 63

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→44.44 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 82865.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Missing residues listed in Remark 465 are due to lack of electron density in those regions.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 569 3 %RANDOM
Rwork0.234 ---
obs0.234 19193 91.6 %-
all-19968 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0428 Å2 / ksol: 0.356485 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.9 Å211.16 Å20 Å2
2--11.9 Å20 Å2
3----23.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 1 85 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 56 2.6 %
Rwork0.372 2115 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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