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- PDB-3ivz: Crystal structure of hyperthermophilic nitrilase -

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Basic information

Entry
Database: PDB / ID: 3ivz
TitleCrystal structure of hyperthermophilic nitrilase
ComponentsNitrilase
KeywordsHYDROLASE / alpha-beta sandwich
Function / homology
Function and homology information


nitrilase / nitrilase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function
: / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRaczynska, J. / Vorgias, C. / Antranikian, G. / Rypniewski, W.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystallographic analysis of a thermoactive nitrilase.
Authors: Raczynska, J.E. / Vorgias, C.E. / Antranikian, G. / Rypniewski, W.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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.pdbx_leaving_atom_flag / _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: Nitrilase
B: Nitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5753
Polymers59,5502
Non-polymers241
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-26 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.174, 59.174, 127.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Nitrilase / Beta ureidopropionase / Beta-alanine synthase


Mass: 29775.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: nit-30, PAB1449, PYRAB13990 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UYV8, beta-ureidopropionase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS RESIDUE AT POSITION 238 IS MORE LIKELY A SER.

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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: 1.87 Å3/Da / Density % sol: 34.06 %
Description: The completeness of the diffraction data was 96.0% in the 1.80-1.76 A resolution shell. Higher resolution data were less complete but they were included in the refinement.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 550MME, 0.2M MgCl2, 0.2M TrisHCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2006
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 1.57→50 Å / Num. obs: 51424 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.8
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.7 / Num. unique all: 984 / Rsym value: 0.193 / % possible all: 16

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0092refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j31.pdb

1j31


Resolution: 1.57→25.91 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.575 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17591 1055 2.1 %RANDOM
Rwork0.13136 ---
obs0.13235 48714 81.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.829 Å2
Baniso -1Baniso -2Baniso -3
1--11.83 Å20 Å20 Å2
2---11.83 Å20 Å2
3---23.65 Å2
Refinement stepCycle: LAST / Resolution: 1.57→25.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 1 126 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9745797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02823.72207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19815754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0761532
X-RAY DIFFRACTIONr_chiral_restr0.1050.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8451.52604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45424209
X-RAY DIFFRACTIONr_scbond_it2.44531687
X-RAY DIFFRACTIONr_scangle_it3.9824.51586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 12 -
Rwork0.345 864 -
obs--19.44 %

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