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Yorodumi- PDB-2gfb: CRYSTAL STRUCTURE OF A CATALYTIC FAB HAVING ESTERASE-LIKE ACTIVITY -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gfb | ||||||
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Title | CRYSTAL STRUCTURE OF A CATALYTIC FAB HAVING ESTERASE-LIKE ACTIVITY | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Golinelli-Pimpaneau, B. / Knossow, M. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystal structure of a catalytic antibody Fab with esterase-like activity. Authors: Golinelli-Pimpaneau, B. / Gigant, B. / Bizebard, T. / Navaza, J. / Saludjian, P. / Zemel, R. / Tawfik, D.S. / Eshhar, Z. / Green, B.S. / Knossow, M. #1: Journal: Mol.Immunol. / Year: 1994 Title: Differences in the Biochemical Properties of Esterolytic Antibodies Correlate with Structural Diversity Authors: Zemel, R. / Schindler, D.G. / Tawfik, D.S. / Eshhar, Z. / Green, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gfb.cif.gz | 628.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gfb.ent.gz | 520.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gfb_validation.pdf.gz | 508.6 KB | Display | wwPDB validaton report |
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Full document | 2gfb_full_validation.pdf.gz | 609.9 KB | Display | |
Data in XML | 2gfb_validation.xml.gz | 73.6 KB | Display | |
Data in CIF | 2gfb_validation.cif.gz | 112.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/2gfb ftp://data.pdbj.org/pub/pdb/validation_reports/gf/2gfb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 141 / 3: CIS PROLINE - PRO B 149 / 4: CIS PROLINE - PRO B 151 / 5: CIS PROLINE - PRO B 200 / 6: CIS PROLINE - PRO C 8 / 7: CIS PROLINE - PRO C 141 / 8: CIS PROLINE - PRO D 149 / 9: CIS PROLINE - PRO D 151 / 10: CIS PROLINE - PRO D 200 / 11: CIS PROLINE - PRO E 8 / 12: CIS PROLINE - PRO E 141 / 13: CIS PROLINE - PRO F 149 / 14: CIS PROLINE - PRO F 151 / 15: CIS PROLINE - PRO F 200 / 16: CIS PROLINE - PRO G 8 / 17: CIS PROLINE - PRO G 141 / 18: CIS PROLINE - PRO H 149 / 19: CIS PROLINE - PRO H 151 / 20: CIS PROLINE - PRO H 200 / 21: CIS PROLINE - PRO I 8 / 22: CIS PROLINE - PRO I 141 / 23: CIS PROLINE - PRO J 149 / 24: CIS PROLINE - PRO J 151 / 25: CIS PROLINE - PRO J 200 / 26: CIS PROLINE - PRO K 8 / 27: CIS PROLINE - PRO K 141 / 28: CIS PROLINE - PRO L 149 / 29: CIS PROLINE - PRO L 151 / 30: CIS PROLINE - PRO L 200 / 31: CIS PROLINE - PRO M 8 / 32: CIS PROLINE - PRO M 141 / 33: CIS PROLINE - PRO N 149 / 34: CIS PROLINE - PRO N 151 / 35: CIS PROLINE - PRO N 200 / 36: CIS PROLINE - PRO O 8 / 37: CIS PROLINE - PRO O 141 / 38: CIS PROLINE - PRO P 149 / 39: CIS PROLINE - PRO P 151 / 40: CIS PROLINE - PRO P 200 | ||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS C AND D, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS E AND F, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS G AND H, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS I AND J, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 5* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS K AND L, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 6* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS M AND N, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX 7* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS O AND P, RESPECTIVELY. |
-Components
#1: Antibody | Mass: 23502.881 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12002892 #2: Antibody | Mass: 23355.168 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 4091056 Sequence details | RESIDUE NUMBERING IS ACCORDING TO KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN AND C. ...RESIDUE NUMBERING IS ACCORDING TO KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN AND C. FOELLER, SEQUENCES OF PROTEINS OF IMMUNOLOGI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 64830 / % possible obs: 93 % / Num. measured all: 115376 / Rmerge(I) obs: 0.072 |
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Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.08 Å / Rmerge(I) obs: 0.143 |
-Processing
Software |
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Refinement | Resolution: 3→7 Å / σ(F): 2 Details: RESIDUES 100A - 103 AND 128 - 136 OF THE HEAVY CHAINS ARE POORLY DEFINED BY THE ELECTRON DENSITY. CARE SHOULD ALSO BE EXERCISED IN INTERPRETING THIS MODEL, DUE TO THE LIMITED RESOLUTION. ...Details: RESIDUES 100A - 103 AND 128 - 136 OF THE HEAVY CHAINS ARE POORLY DEFINED BY THE ELECTRON DENSITY. CARE SHOULD ALSO BE EXERCISED IN INTERPRETING THIS MODEL, DUE TO THE LIMITED RESOLUTION. REFINEMENT AT HIGHER RESOLUTION IS PRESENTLY BEING PURSUED; IN THIS WORK, RESIDUE 114 OF THE HEAVY CHAIN, WHICH IS MISSING IN THIS ENTRY, HAS BEEN LOCATED, WHICH LEADS TO MODIFICATION OF THE ATOMIC POSITIONS OF THE SURROUNDING RESIDUES.
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Refinement step | Cycle: LAST / Resolution: 3→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2 |