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- PDB-1nba: CRYSTAL STRUCTURE ANALYSIS, REFINEMENT AND ENZYMATIC REACTION MEC... -

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Basic information

Entry
Database: PDB / ID: 1nba
TitleCRYSTAL STRUCTURE ANALYSIS, REFINEMENT AND ENZYMATIC REACTION MECHANISM OF N-CARBAMOYLSARCOSINE AMIDOHYDROLASE FROM ARTHROBACTER SP. AT 2.0 ANGSTROMS RESOLUTION
ComponentsN-CARBAMOYLSARCOSINE AMIDOHYDROLASE
KeywordsHYDROLASE(IN LINEAR AMIDES)
Function / homology
Function and homology information


N-carbamoylsarcosine amidase / N-carbamoylsarcosine amidase activity / creatinine catabolic process
Similarity search - Function
: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-carbamoylsarcosine amidase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRomao, M.J. / Turk, D. / Gomis-Ruth, F.-Z. / Huber, R. / Schumacher, G. / Mollering, H. / Russmann, L.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution.
Authors: Romao, M.J. / Turk, D. / Gomis-Ruth, F.X. / Huber, R. / Schumacher, G. / Mollering, H. / Russmann, L.
History
DepositionMay 18, 1992Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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-CARBAMOYLSARCOSINE AMIDOHYDROLASE
B: N-CARBAMOYLSARCOSINE AMIDOHYDROLASE
C: N-CARBAMOYLSARCOSINE AMIDOHYDROLASE
D: N-CARBAMOYLSARCOSINE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7218
Polymers116,3374
Non-polymers3844
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint-174 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.220, 122.290, 70.870
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: ALA A 172 - THR A 173 OMEGA =352.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA B 172 - THR B 173 OMEGA =354.44 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA C 172 - THR C 173 OMEGA =352.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA D 172 - THR D 173 OMEGA =355.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein
N-CARBAMOYLSARCOSINE AMIDOHYDROLASE


Mass: 29084.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / References: UniProt: P32400, N-carbamoylsarcosine amidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion / Details: drop-0.002ml, reservoir-0.003ml
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
21.25 Mmagnesium sulfate1drop
320 mMtrimethylphosphate1reservoir0.003ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 9999 Å / Num. obs: 62120 / % possible obs: 73.2 % / Num. measured all: 147634 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 40.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.186 / Rfactor obs: 0.186 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 20 431 8304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 56641 / Rfactor obs: 0.186 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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