4L6E | pdb_00004l6e

Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics Consortium (NESG) Target HR9193b

PDB DOI: https://doi.org/10.2210/pdb4L6E/pdb

Classification: LIGASE, ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-12 Released: 2013-06-26
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Mao, L., Xiao, R., Maglaqui, M., Kogan, S., Wang, H., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.222 (Depositor), 0.231 (DCC)
R-Value Work:
0.197 (Depositor), 0.205 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2.

Vorobiev, S., Su, M., Seetharaman, J., Mao, L., Xiao, R., Maglaqui, M., Kogan, S., Wang, H., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 18.71 kDa
Atom Count: 1,072
Modeled Residue Count: 124
Deposited Residue Count: 155
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase RanBP2	A	155	Homo sapiens	Mutation(s): 0 Gene Names: NUP358, RANBP2 EC: 6.3.2 (PDB Primary Data), 5.2.1.8 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49792 (Homo sapiens) Explore P49792 Go to UniProtKB: P49792
PHAROS: P49792 GTEx: ENSG00000153201
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.222 (Depositor), 0.231 (DCC)
R-Value Work: 0.197 (Depositor), 0.205 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.481	α = 90
b = 69.481	β = 90
c = 152.55	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary