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

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Basic information

Entry
Database: PDB / ID: 3klc
TitleCrystal structure of hyperthermophilic nitrilase
ComponentsBeta ureidopropionase (Beta-alanine synthase)
KeywordsHYDROLASE / alpha-beta sandwich
Function / homology
Function and homology information


nitrilase / indole-3-acetonitrile nitrilase activity
Similarity search - Function
: / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / BROMIDE ION / Nitrilase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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
DepositionNov 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Beta ureidopropionase (Beta-alanine synthase)
B: Beta ureidopropionase (Beta-alanine synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,73418
Polymers59,5502
Non-polymers1,18316
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-27 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.283, 59.283, 129.196
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 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 33% PEG 550MME, 0.2M Mg(CH3COOH)2 and 0.2 TrisHCl. The crystal soaked with 1M KBr for ~1 minute, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.91163, 0.91994, 0.88557
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2006
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911631
20.919941
30.885571
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.581
11-H, K, -L20.419
ReflectionResolution: 1.76→50 Å / Num. all: 37990 / Num. obs: 37990 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 32
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2 / Rsym value: 0.431 / % possible all: 30.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KI8

3ki8


Resolution: 1.76→43.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.592 / SU ML: 0.079 / Isotropic thermal model: Mixed isotropic/anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19214 1940 5.1 %RANDOM
Rwork0.15534 ---
obs0.15729 35951 85.89 %-
all-36004 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.583 Å2
Baniso -1Baniso -2Baniso -3
1--22.21 Å20 Å20 Å2
2---22.21 Å20 Å2
3---44.43 Å2
Refinement stepCycle: LAST / Resolution: 1.76→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 22 218 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9765784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.215522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63523.816207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8915757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.061532
X-RAY DIFFRACTIONr_chiral_restr0.1120.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213264
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_it0.9431.52609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54724206
X-RAY DIFFRACTIONr_scbond_it2.71831679
X-RAY DIFFRACTIONr_scangle_it4.1034.51575
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 50 -
Rwork0.592 958 -
obs--30.93 %

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