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- PDB-3n5f: Crystal Structure of L-N-carbamoylase from Geobacillus stearother... -

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Basic information

Entry
Database: PDB / ID: 3n5f
TitleCrystal Structure of L-N-carbamoylase from Geobacillus stearothermophilus CECT43
ComponentsN-carbamoyl-L-amino acid hydrolase
KeywordsHYDROLASE / Carbamoylase / hinge domain / M20 peptidase family / evolution / binding residue / dimerization domain
Function / homology
Function and homology information


N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / cobalt ion binding / manganese ion binding / identical protein binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / : / ISOPROPYL ALCOHOL / N-carbamoyl-L-amino acid hydrolase
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGarcia-Pino, A. / Martinez-Rodriguez, S. / Gavira, J.A.
Citation
Journal: J.Bacteriol. / Year: 2012
Title: Mutational and structural analysis of L-N-carbamoylase reveals new insights into a peptidase m20/m25/m40 family member.
Authors: Martinez-Rodriguez, S. / Garcia-Pino, A. / Las Heras-Vazquez, F.J. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Garcia-Ruiz, J.M. / Loris, R. / Gavira, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary crystallographic studies of the recombinant L-N-carbamoylase from Geobacillus stearothermophilus CECT43.
Authors: Martinez-Rodriguez, S. / Garcia-Pino, A. / Las Heras-Vazquez, F.J. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Loris, R. / Garcia-Ruiz, J.M. / Gavira, J.A.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: N-carbamoyl-L-amino acid hydrolase
B: N-carbamoyl-L-amino acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7167
Polymers88,3412
Non-polymers3755
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-39 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.208, 211.683, 43.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

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Components

#1: Protein N-carbamoyl-L-amino acid hydrolase / L-carbamoylase


Mass: 44170.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Strain: CECT43 / Gene: amaB / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53389, N-carbamoyl-L-amino-acid hydrolase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % iso-propanol, 0.1 M sodium cacodylate pH 6.5 and 0.6 M trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 3, 2006 / Details: Kappa configuration
RadiationMonochromator: Montel Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.75→73.89 Å / Num. all: 25512 / Num. obs: 25512 / % possible obs: 99.1 % / Redundancy: 7.26 % / Rmerge(I) obs: 0.1238 / Rsym value: 0.1238 / Net I/σ(I): 15.05
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.2578 / Mean I/σ(I) obs: 4.16 / Rsym value: 0.2578 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z2L

1z2l


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.811 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 13.946 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27579 1271 5.1 %RANDOM
Rwork0.19266 ---
obs0.1968 23771 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.701 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2---0.26 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5993 0 15 128 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226201
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.968450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8523.457243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.07115979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8741546
X-RAY DIFFRACTIONr_chiral_restr0.0980.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214704
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_it0.6041.54051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07526485
X-RAY DIFFRACTIONr_scbond_it1.58132150
X-RAY DIFFRACTIONr_scangle_it2.6954.51956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 87 -
Rwork0.273 1495 -
obs--87.99 %

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