3PUT | pdb_00003put

Crystal Structure of the CERT START domain (mutant V151E) from Rhizobium etli at the resolution 1.8A, Northeast Structural Genomics Consortium Target ReR239.

PDB DOI: https://doi.org/10.2210/pdb3PUT/pdb

Classification: Structure Genomics, unknown function
Organism(s): Rhizobium etli CFN 42
Mutation(s): Yes

Deposited: 2010-12-06 Released: 2010-12-22
Deposition Author(s): Kuzin, A., Chen, Y., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.222 (Depositor), 0.218 (DCC)
R-Value Work:
0.177 (Depositor), 0.172 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the CERT START domain (mutant V151E) from Rhizobium etli at the resolution 1.8A, Northeast Structural Genomics Consortium Target ReR239.

Kuzin, A., Chen, Y., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 38.63 kDa
Atom Count: 2,663
Modeled Residue Count: 305
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical conserved protein	A, B	166	Rhizobium etli CFN 42	Mutation(s): 1 Gene Names: RHE_CH02426
UniProt
Find proteins for Q2K7I2 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2K7I2 Go to UniProtKB: Q2K7I2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2K7I2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 1.83 Å
R-Value Free: 0.222 (Depositor), 0.218 (DCC)
R-Value Work: 0.177 (Depositor), 0.172 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.515	α = 90
b = 76.931	β = 97.64
c = 55.742	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-22
Changes: Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-27
Changes: Structure summary