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- PDB-1j2u: Creatininase Zn -

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Basic information

Entry
Database: PDB / ID: 1j2u
TitleCreatininase Zn
Componentscreatinine amidohydrolase
KeywordsHYDROLASE / creatine / creatinine
Function / homology
Function and homology information


creatininase / creatinine catabolic process / creatininase activity / 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 / D-Fourier / Resolution: 1.85 Å
AuthorsYoshimoto, T. / Tanaka, N. / Kanada, N. / Inoue, T. / Nakajima, Y. / Haratake, M. / Nakamura, K.T. / Xu, Y. / Ito, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
Authors: Yoshimoto, T. / Tanaka, N. / Kanada, N. / Inoue, T. / Nakajima, Y. / Haratake, M. / Nakamura, K.T. / Xu, Y. / Ito, K.
History
DepositionJan 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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_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: creatinine amidohydrolase
B: creatinine amidohydrolase
C: creatinine amidohydrolase
D: creatinine amidohydrolase
E: creatinine amidohydrolase
F: creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,33828
Polymers171,5936
Non-polymers1,74622
Water23,6901315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24850 Å2
ΔGint-709 kcal/mol
Surface area51990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.114, 151.449, 167.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer. Six subunits (one hexamer) exist in an asymmetric unit.

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Components

#1: Protein
creatinine amidohydrolase / diagnase


Mass: 28598.789 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pBluescript KS(-) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1315 / 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: 3.77 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Li sulfate, 0.1M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135 mg/mlprotein1drop
20.1 MHEPES1droppH7.5
31.5 Mlithium sulfate1reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 218133 / % possible obs: 98.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.7
Reflection shellHighest resolution: 1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.335 / % possible all: 99.7
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 99.7 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: D-Fourier / Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.184 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20131 10941 5 %RANDOM
Rwork0.18631 ---
obs0.18707 207021 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.062 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 62 1315 13305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112268
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211238
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.96816698
X-RAY DIFFRACTIONr_angle_other_deg0.707326082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.00331536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.573152137
X-RAY DIFFRACTIONr_chiral_restr0.0740.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022448
X-RAY DIFFRACTIONr_nbd_refined0.2220.32648
X-RAY DIFFRACTIONr_nbd_other0.1990.310682
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.51198
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2890.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.32
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6381.57668
X-RAY DIFFRACTIONr_mcangle_it1.179212366
X-RAY DIFFRACTIONr_scbond_it1.72134600
X-RAY DIFFRACTIONr_scangle_it2.8414.54332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 794
Rwork0.258 15312
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.072
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.269

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