4M6D | pdb_00004m6d

Crystal structure of the aptamer minF-lysozyme complex.

PDB DOI: https://doi.org/10.2210/pdb4M6D/pdb
NAKB: 4M6D

Classification: Hydrolase/RNA
Organism(s): Gallus gallus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-09 Released: 2013-12-11
Deposition Author(s): Malashkevich, V.N., Padlan, F.C., Toro, R., Girvin, M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.216 (Depositor), 0.212 (DCC)
R-Value Work:
0.165 (Depositor), 0.172 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the aptamer minF-lysozyme complex.

Malashkevich, V.N., Padlan, F.C., Toro, R., Girvin, M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 173.12 kDa
Atom Count: 11,432
Modeled Residue Count: 1,024
Deposited Residue Count: 1,044
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, C, E, G, I A, C, E, G, I, K	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ, lyz1 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
aptamer	B, D, F, H, J B, D, F, H, J, L	45	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.216 (Depositor), 0.212 (DCC)
R-Value Work: 0.165 (Depositor), 0.172 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.914	α = 118.59
b = 132.289	β = 96.39
c = 131.539	γ = 96.27

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Malashkevich, V.N.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2018-01-24
Changes: Advisory, Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.