3DB5 | pdb_00003db5

Crystal structure of methyltransferase domain of human PR domain-containing protein 4

PDB DOI: https://doi.org/10.2210/pdb3DB5/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-30 Released: 2008-08-12
Deposition Author(s): Amaya, M.F., Zeng, H., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.298 (Depositor), 0.287 (DCC)
R-Value Work:
0.222 (Depositor), 0.219 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of methyltransferase domain of human PR domain-containing protein 4.

Zeng, H., Amaya, M.F., Loppnau, P., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 35.05 kDa
Atom Count: 2,201
Modeled Residue Count: 258
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain zinc finger protein 4	A, B	151	Homo sapiens	Mutation(s): 0 Gene Names: PRDM4, PFM1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKN5 (Homo sapiens) Explore Q9UKN5 Go to UniProtKB: Q9UKN5
PHAROS: Q9UKN5 GTEx: ENSG00000110851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.298 (Depositor), 0.287 (DCC)
R-Value Work: 0.222 (Depositor), 0.219 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.294	α = 90
b = 107.294	β = 90
c = 133.642	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Arrowsmith, C.H.

Plotnikov, A.N.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.