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- PDB-1kp0: The Crystal Structure Analysis of Creatine Amidinohydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 1kp0
TitleThe Crystal Structure Analysis of Creatine Amidinohydrolase from Actinobacillus
ComponentsCREATINE AMIDINOHYDROLASE
KeywordsHYDROLASE / Alpha Betal / 3-Layer(aba) Sandwich
Function / homology
Function and homology information


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
Biological speciesActinobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPadmanabhan, B. / Paehler, A. / Horikoshi, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of creatine amidinohydrolase from Actinobacillus.
Authors: Padmanabhan, B. / Paehler, A. / Horikoshi, M.
History
DepositionDec 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence an appropriate sequence database reference was not available at the time of processing. ...sequence an appropriate sequence database reference was not available at the time of processing. the authors state that the sequence was derived from the crystal structure. AT THE END OF FINAL REFINEMENT, RESIDUES (ASP,ASN,GLU, AND GLN) WHICH ARE CONSERVED BETWEEN P.PUTIDA AND BACILLUS CREATINASE WERE TREATED AS THE SAME CORRESPONDING RESIDUES AT EQUIVALENT POSITIONS IN AC.BACILLUS CREATINASE OR OTHERWISE TREATED AS ASX OR GLX. GLX: 5,7,13,21,28,68,72,119,134,136,149,154,163,168 GLX: 204,240,267,268,275,278,289,310,345 ASX: 29,39,71,94,130,164,199,208,236,270,306,329,362,384

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREATINE AMIDINOHYDROLASE
B: CREATINE AMIDINOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)89,4532
Polymers89,4532
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-39 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.263, 113.624, 191.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CREATINE AMIDINOHYDROLASE


Mass: 44726.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Actinobacillus (bacteria) / Genus: Actinobacillus / References: UniProt: Q7SIB5, creatinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.26 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110.0 mg/mlprotein1drop
210 %PEG60001reservoir
30.1 Msodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 33916 / Num. obs: 33902 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 167670 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.151

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DPSdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1CHM

1chm


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1672 -Random
Rwork0.188 ---
all0.191 33576 --
obs0.191 33576 99.6 %-
Solvent computationSolvent model: flat model / Bsol: 13.5746 Å2 / ksol: 0.310792 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å20 Å2
2--3.18 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 0 118 6586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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 DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.682.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 273 5 %
Rwork0.26 5234 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.191 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.321 / Rfactor Rwork: 0.26

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