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- PDB-1q3k: Crystal structure of creatinine amidohydrolase (creatininase) -

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Basic information

Entry
Database: PDB / ID: 1q3k
TitleCrystal structure of creatinine amidohydrolase (creatininase)
Componentscreatininase
KeywordsHYDROLASE / alpha-beta-fold
Function / homology
Function and homology information


creatininase / creatininase activity / creatinine catabolic process / creatine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / riboflavin biosynthetic process / manganese ion binding / zinc ion binding
Similarity search - Function
Creatinine amidohydrolase / Creatininase / Creatininase/formamide hydrolase / Creatininase-like superfamily / Creatinine amidohydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Creatinine amidohydrolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBeuth, B. / Niefind, K. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of creatininase from Pseudomonas putida: A novel fold and a case of convergent evolution
Authors: Beuth, B. / Niefind, K. / Schomburg, D.
History
DepositionJul 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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_asym_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: creatininase
B: creatininase
C: creatininase
D: creatininase
E: creatininase
F: creatininase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,72522
Polymers170,5716
Non-polymers1,15316
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24560 Å2
ΔGint-586 kcal/mol
Surface area50110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.392, 94.084, 114.746
Angle α, β, γ (deg.)90.00, 104.62, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
creatininase / E.C.3.5.2.10 / creatinine amidohydrolase


Mass: 28428.539 Da / Num. of mol.: 6 / Fragment: enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P83772, creatininase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, ethanol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
30.1 MMOPS1reservoiror 0.1M HEPES, pH7.5
422 %(v/v)ethanol1reservoir
520 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 24, 2000
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 90353 / Num. obs: 71469 / % possible obs: 79.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 31.5 Å2 / Rsym value: 0.039 / Net I/σ(I): 22.5
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.309 / % possible all: 52.5
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. measured all: 223797 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 52.5 % / Rmerge(I) obs: 0.309

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3529 -random
Rwork0.207 ---
all0.209 89333 --
obs0.209 71026 79.5 %-
Displacement parametersBiso mean: 38 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12000 0 36 724 12760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.02
X-RAY DIFFRACTIONr_angle_refined_deg1.542
X-RAY DIFFRACTIONr_chiral_restr0.103
LS refinement shellResolution: 2.1→2.15 Å
RfactorNum. reflection
Rfree0.365 169
Rwork0.294 -
obs-3305
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.542

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