+Open data
-Basic information
Entry | Database: PDB / ID: 2rtj | |||||||||
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Title | STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I4122 | |||||||||
Components | STREPTAVIDIN | |||||||||
Keywords | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-GLYCOLURIL / PH 2.50 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | |||||||||
Authors | Katz, B.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. Authors: Katz, B.A. #1: Journal: J.Biol.Chem. / Year: 1997 Title: In Crystals of Complexes of Streptavidin with Peptide Ligands Containing the Hpq Sequence the Pka of the Peptide Histidine is Less Than 3.0 Authors: Katz, B.A. / Cass, R.T. #2: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity Authors: Katz, B.A. / Liu, B. / Cass, R.T. #3: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #4: Journal: J.Biol.Chem. / Year: 1995 Title: Topochemical Catalysis Achieved by Structure-Based Ligand Design Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #5: Journal: Chem.Biol. / Year: 1995 Title: Topochemistry for Preparing Ligands that Dimerize Receptors Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #6: Journal: Biochemistry / Year: 1995 Title: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence Authors: Katz, B.A. #7: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rtj.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rtj.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 2rtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rtj_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 2rtj_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 2rtj_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 2rtj_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/2rtj ftp://data.pdbj.org/pub/pdb/validation_reports/rt/2rtj | HTTPS FTP |
-Related structure data
Related structure data | 2izaC 2izbC 2izcC 2izdC 2izeC 2izfC 2izgC 2izhC 2iziC 2izjC 2izkC 2izlC 2rtaC 2rtbC 2rtcC 2rtdC 2rteC 2rtfC 2rtgC 2rthC 2rtiC 2rtkC 2rtlC 2rtmC 2rtnC 2rtoC 2rtpC 2rtqC 2rtrC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14181.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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#2: Chemical | ChemComp-GLL / |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 38.2 % Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE INTENSITY OF REFLECTION H (M.G.ROSSMANN, A.G.W.LESLIE, S.S.ABDEL-MEGUID, T.TSUKIHARA, ...Description: REJECTION CRITERIA: (I(H)I - ) > [0.30 * ( | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 2.5 Details: ROOM TEMPERATURE, PH 2.50. SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.50. | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 23182 / % possible obs: 82 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.43→1.49 Å / Redundancy: 2.7 % / % possible all: 31.6 |
Reflection | *PLUS Highest resolution: 1.4 Å / Num. measured all: 63148 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Highest resolution: 1.4 Å / σ(F): 0.5 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT FOR C AND O), GLY 26, ALA 35 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, C, O, CB, HB1, HB2), ASP 36 ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT FOR C AND O), GLY 26, ALA 35 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, C, O, CB, HB1, HB2), ASP 36 (CG, OD1, AND OD), GLU 44 (CG, HG1, HG2, CD, OE1, OE2) ALA 46 (CA, HA, C, O, CB, HB1, HB2, HB3), VAL 47, GLY 48, ASN 49, ALA 50, GLU 51 SER 52 (SIDE CHAIN), ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG, CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY 99, ALA 100, GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22), GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O, CD, OE1, OE2) ALA 117, ASN 118 (SIDE CHAIN), LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3), LYS 134 (CB, HB1, HB2, CG, HG1, HG2, CD, HD1, HD2), LYS 134 (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3), PRO 135 RESIDUES TYR 60 TO SER 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES ASP 61 TO SER 69 ALSO UNDERGOES CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: PHE 29, LEU 73, HIS 87, GLN 107, LEU 110, AND LYS 132. DISORDERED SOLVENTS ARE: HOH 136 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION NUMBER 2 HOH 207 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 354 HOH 305 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 546 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 558 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 624 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13 GLU 14 ALA 15 (EXCEPT FOR C AND O) GLY 26 ALA 35 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, C, O, CB, HB1, HB2) ASP 36 (CG, OD1, AND OD) GLU 44 (CG, HG1, HG2, CD, OE1, OE2) ALA 46 (CA, HA, C, O, CB, HB1, HB2, HB3) VAL 47 GLY 48 ASN 49 ALA 50 GLU 51 SER 52 (SIDE CHAIN) ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG, CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY 99 ALA 100 GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O, CD, OE1, OE2) ALA 117 ASN 118 (SIDE CHAIN) LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3), LYS 134 (CB, HB1, HB2, CG, HG1, HG2, CD, HD1, HD2) LYS 134 (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3) PRO 135 RESIDUES TYR 60 TO SER 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES ASP 61 TO SER 69 ALSO UNDERGOES CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION.
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Refinement step | Cycle: LAST / Highest resolution: 1.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.49 Å / % reflection obs: 31.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.206 |