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- PDB-1chm: ENZYMATIC MECHANISM OF CREATINE AMIDINOHYDROLASE AS DEDUCED FROM ... -

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Basic information

Entry
Database: PDB / ID: 1chm
TitleENZYMATIC MECHANISM OF CREATINE AMIDINOHYDROLASE AS DEDUCED FROM CRYSTAL STRUCTURES
ComponentsCREATINE AMIDINOHYDROLASE
KeywordsCREATINASE
Function / homology
Function and homology information


creatinase / creatinase activity
Similarity search - Function
Creatinase, C-terminal / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Creatinase, C-terminal / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBAMOYL SARCOSINE / Creatinase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHoeffken, H.W. / Knof, S.H. / Bartlett, P.A. / Huber, R. / Moellering, H. / Schumacher, G.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures.
Authors: Coll, M. / Knof, S.H. / Ohga, Y. / Messerschmidt, A. / Huber, R. / Moellering, H. / Russmann, L. / Schumacher, G.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure Determination, Refinement and Molecular Model of Creatine Amidinohydrolase from Pseudomonas Putida
Authors: Hoeffken, H.W. / Knof, S.H. / Bartlett, P.A. / Huber, R. / Moellering, H. / Schumacher, G.
History
DepositionJul 19, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: CREATINE AMIDINOHYDROLASE
B: CREATINE AMIDINOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9304
Polymers90,6662
Non-polymers2642
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-27 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 110.550, 62.630
Angle α, β, γ (deg.)90.00, 102.22, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: GLU B 383 - ASN B 384 OMEGA =212.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein CREATINE AMIDINOHYDROLASE


Mass: 45333.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P38488, creatinase
#2: Chemical ChemComp-CMS / CARBAMOYL SARCOSINE


Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal grow
*PLUS
pH: 5.4 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
220 %(w/v)PEG600011
30.2 Msodium phosphate11
40.01 Minhibitor11

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Data collection

Reflection
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 99 Å / Num. obs: 26026 / Num. measured all: 79941 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 2.52 Å / % possible obs: 41.5 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.9→8 Å / Rfactor Rwork: 0.177
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6374 0 18 394 6786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.033
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor Rwork: 0.183 / Highest resolution: 2.5 Å / Num. reflection obs: 22809
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.9

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