3BDU | pdb_00003bdu

Crystal structure of protein Q6D8G1 at the resolution 1.9 A. Northeast Structural Genomics Consortium target EwR22A.

PDB DOI: https://doi.org/10.2210/pdb3BDU/pdb

Classification: LIPOPROTEIN
Organism(s): Pectobacterium atrosepticum SCRI1043
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-15 Released: 2007-11-27
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Fang, Y., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.247 (Depositor), 0.257 (DCC)
R-Value Work:
0.210 (Depositor), 0.221 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of protein Q6D8G1 at the resolution 1.9 A.

Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Fang, Y., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 50.77 kDa
Atom Count: 3,009
Modeled Residue Count: 366
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein	A, B, C, D, E A, B, C, D, E, F, G	62	Pectobacterium atrosepticum SCRI1043	Mutation(s): 0 Gene Names: ECA1013
UniProt
Find proteins for Q6D8G1 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D8G1 Go to UniProtKB: Q6D8G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6D8G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.247 (Depositor), 0.257 (DCC)
R-Value Work: 0.210 (Depositor), 0.221 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.974	α = 90
b = 79.077	β = 96.295
c = 48.472	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-12-25
Changes: Advisory, Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary