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- PDB-3a6f: W174F mutant creatininase, Type II -

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Basic information

Entry
Database: PDB / ID: 3a6f
TitleW174F mutant creatininase, Type II
ComponentsCreatinine amidohydrolase
KeywordsHYDROLASE / creatinine amidohydrolase / urease-related amidohydrolase superfamily
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
CACODYLATE ION / : / Creatinine amidohydrolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNakajima, Y. / Yamashita, K. / Ito, K. / Yoshimoto, T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
Authors: Yamashita, K. / Nakajima, Y. / Matsushita, H. / Nishiya, Y. / Yamazawa, R. / Wu, Y.F. / Matsubara, F. / Oyama, H. / Ito, K. / Yoshimoto, T.
History
DepositionAug 31, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)172,90324
Polymers171,3596
Non-polymers1,54418
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22120 Å2
ΔGint-111 kcal/mol
Surface area50560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.3, 164.3, 163.9
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Creatinine amidohydrolase / creatininase


Mass: 28559.754 Da / Num. of mol.: 6 / Mutation: W174F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P83772, creatininase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 45% PEG200, 20mM Magnesium chloride, 100mM Sodium cacodylate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2006 / Details: Rhodium coated silicon single crystal
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 242993 / Num. obs: 242993 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 41.8
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 10 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.6 / Num. unique all: 24075 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2T

1j2t


Resolution: 1.78→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The diffraction data was detwined with twin fraction of 0.463
RfactorNum. reflection% reflectionSelection details
Rfree0.257 12155 -random
Rwork0.235 ---
all-242302 --
obs-242302 99.9 %-
Displacement parametersBiso mean: 25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11850 0 42 764 12656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.834
LS refinement shellResolution: 1.78→1.84 Å
RfactorNum. reflection% reflection
Rfree0.356 1195 -
Rwork0.336 --
obs-23833 99 %

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