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- PDB-3a6d: Creatininase complexed with 1-methylguanidine -

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Basic information

Entry
Database: PDB / ID: 3a6d
TitleCreatininase complexed with 1-methylguanidine
ComponentsCreatinine amidohydrolase
KeywordsHYDROLASE / creatinine amidohydrolase / urease-related amidohydrolase superfamily / closed form
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
1-METHYLGUANIDINE / : / Creatinine amidohydrolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_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)174,48342
Polymers171,5936
Non-polymers2,89036
Water19,6001088
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21550 Å2
ΔGint-117 kcal/mol
Surface area50770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.4, 152.7, 167.5
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Creatinine amidohydrolase / creatininase


Mass: 28598.789 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 1124 molecules

#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-MGX / 1-METHYLGUANIDINE


Mass: 73.097 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H7N3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M lithium sulfate, 5mM 1-methylguanidine, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 203658 / Num. obs: 203658 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.8 / Num. unique all: 18439 / % possible all: 90.3

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2T

1j2t


Resolution: 1.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 10240 -random
Rwork0.192 ---
all-203364 --
obs-203364 98.8 %-
Displacement parametersBiso mean: 30.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11891 0 132 1088 13111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.817
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.272 927 -
Rwork0.264 --
obs-17328 89.5 %

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