1SBK | pdb_00001sbk

X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.

PDB DOI: https://doi.org/10.2210/pdb1SBK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-02-10 Released: 2004-02-24
Deposition Author(s): Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Lee, I., Forouhar, F., Ma, L., Chiang, Y., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.223 (Depositor), 0.225 (DCC)
R-Value Observed:
0.223 (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

X-ray Structure of YDII_ECOLI Northeast Structural Genomics Consortium Target ER29

Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Lee, I., Forouhar, F., Ma, L., Chiang, Y., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 65.28 kDa
Atom Count: 4,693
Modeled Residue Count: 552
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ydiI	A, B, C, D	144	Escherichia coli	Mutation(s): 4 Gene Names: YDII, B1686 EC: 3.1.2.28
UniProt
Find proteins for P77781 (Escherichia coli (strain K12)) Explore P77781 Go to UniProtKB: P77781
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77781
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.223 (Depositor), 0.225 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.642	α = 90
b = 61.196	β = 104.66
c = 93.008	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-02-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2004-02-24
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-11-20
Changes: Structure summary