6XUO | pdb_00006xuo

mature recombinant horse NGF

PDB DOI: https://doi.org/10.2210/pdb6XUO/pdb

Classification: CYTOKINE
Organism(s): Equus caballus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-20 Released: 2020-01-29
Deposition Author(s): Kalnins, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.266 (Depositor), 0.275 (DCC)
R-Value Work:
0.219 (Depositor), 0.222 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Mature horse nerve growth factor at 2.8 angstrom resolution

Kalnins, G., Tars, K.

To be published.

Macromolecule Content

Total Structure Weight: 25.11 kDa
Atom Count: 840
Modeled Residue Count: 107
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nerve growth factor	A	224	Equus caballus	Mutation(s): 0 Gene Names: NGF
UniProt
Find proteins for F6SVV7 (Equus caballus) Explore F6SVV7 Go to UniProtKB: F6SVV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6SVV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.266 (Depositor), 0.275 (DCC)
R-Value Work: 0.219 (Depositor), 0.222 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.49	α = 90
b = 108.49	β = 90
c = 108.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, 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.