[English] 日本語
Yorodumi- PDB-2kau: THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kau | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ANGSTROMS RESOLUTION | ||||||
Components |
| ||||||
Keywords | HYDROLASE / NICKEL METALLOENZYME / HYDROLASE (UREA AMIDO) | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. | ||||||
Citation | Journal: Science / Year: 1995 Title: The crystal structure of urease from Klebsiella aerogenes. Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. #1: Journal: Science / Year: 1995 Title: Requirement of Carbon Dioxide for in Vitro Assembly of the Urease Nickel Metallocenter Authors: Park, I.-S. / Hausinger, R.P. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Preliminary Crystallographic Studies of Urease from Jack Bean and from Klebsiella Aerogenes Authors: Jabri, E. / Lee, M.H. / Hausinger, R.P. / Karplus, P.A. | ||||||
History |
| ||||||
Remark 700 | SHEET THE ACTIVE SITE AND BI-NICKEL METALLOCENTER ARE LOCATED IN CHAIN C AT THE C-TERMINUS OF THE ...SHEET THE ACTIVE SITE AND BI-NICKEL METALLOCENTER ARE LOCATED IN CHAIN C AT THE C-TERMINUS OF THE STRANDS IN AN ALPHA-BETA BARREL. THIS BARREL IS STRUCTURALLY HOMOLOGOUS TO THAT OF ADENOSINE DEAMINASE, A MONO-ZINC METALLOENZYME. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2kau.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2kau.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 2kau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kau_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2kau_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 2kau_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2kau_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/2kau ftp://data.pdbj.org/pub/pdb/validation_reports/ka/2kau | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO C 282 / 2: CIS PROLINE - PRO C 303 / 3: CIS PROLINE - PRO C 470 4: RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. IT COORDINATES NI C 774 THROUGH ITS TERMINAL O ATOMS | ||||||||
Details | THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C), FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. THE GAMMA CHAIN WAS CHOSEN AS CHAIN A BECAUSE IT HAS SEQUENCE HOMOLOGY TO THE N-TERMINUS OF THE ONE-SUBUNIT JACK BEAN UREASES, WHEREAS THE K. AEROGENES ALPHA CHAIN C HAS SEQUENCE HOMOLOGY TO THE C-TERMINUS OF JACK BEAN UREASE. THREE UNITS (A, B, C) PACK TIGHTLY AT THE CRYSTALLOGRAPHIC THREE-FOLD TO FORM A TRIMER OF TRIMERS OBSERVED IN SOLUTION. SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. TRIMER 2 OF TRIMER OF TRIMERS APPLIED TO RESIDUES: A 1 .. A 100 SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 1 1.000000 0.000000 0.000000 0.00000 APPLIED TO RESIDUES: B 1 .. B 101 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 2 1.000000 0.000000 0.000000 0.00000 APPLIED TO RESIDUES: C 1 .. C 767 SYMMETRY1 3 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 3 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 3 1.000000 0.000000 0.000000 0.00000 TRIMER 3 OF TRIMER OF TRIMERS APPLIED TO RESIDUES: A 1 .. A 100 SYMMETRY1 4 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 4 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 4 0.000000 1.000000 0.000000 0.00000 APPLIED TO RESIDUES: B 1 .. B 101 SYMMETRY1 5 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 5 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 1.000000 0.000000 0.00000 APPLIED TO RESIDUES: C 1 .. C 767 SYMMETRY1 6 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 6 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 6 0.000000 1.000000 0.000000 0.00000 |
-Components
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREC / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18316, urease | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 11712.239 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREB / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18315, urease | ||||||
#3: Protein | Mass: 60409.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18314, urease | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLAT | Nonpolymer details | NI C 774 IS COORDINATED BY ND1 HIS C 246, NE2 HIS C 272, AND O1 LYS C 217 IN A PSEUDO TETRAHEDRAL ...NI C 774 IS COORDINATE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 Å |
---|---|
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 58334 / % possible obs: 93 % / Redundancy: 7 % / Rmerge(I) obs: 0.089 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 386731 / Rmerge(I) obs: 0.089 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→10 Å / σ(F): 0 Details: RESIDUES 308 - 335 IN CHAIN C HAVE HIGH B-FACTORS. THEY CORRESPOND TO A MOBILE LOOP NEAR THE ACTIVE SITE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |