7ULB | pdb_00007ulb

recombinant Mambalgin-1

PDB DOI: https://doi.org/10.2210/pdb7ULB/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Dendraspis polylepis polylepis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-04 Released: 2023-05-03
Deposition Author(s): Xu, J., Lei, X., Chen, L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.267 (Depositor), 0.271 (DCC)
R-Value Work:
0.217 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure of recombinant mambalgin at 2.49 Angstroms resolution.

Xu, J., Lei, X., Chen, L.

To be published.

Macromolecule Content

Total Structure Weight: 30.39 kDa
Atom Count: 1,890
Modeled Residue Count: 235
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mambalgin-1	A, B, C, D	66	Dendraspis polylepis polylepis	Mutation(s): 0
UniProt
Find proteins for P0DKR6 (Dendroaspis polylepis polylepis) Explore P0DKR6 Go to UniProtKB: P0DKR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DKR6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.267 (Depositor), 0.271 (DCC)
R-Value Work: 0.217 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.984	α = 90
b = 80.753	β = 90.47
c = 54.032	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM064642

Revision History (Full details and data files)

Version 1.0: 2023-05-03
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.