2H1J | pdb_00002h1j

3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals grown by microfluidic seeding

PDB DOI: https://doi.org/10.2210/pdb2H1J/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-05-16 Released: 2006-06-13
Deposition Author(s): Gerdts, C.J., Tereshko, V., Dementieva, I., Collart, F., Joachimiak, A., Kossiakoff, A., Ismagilov, R.F., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization.

Gerdts, C.J., Tereshko, V., Yadav, M.K., Dementieva, I., Collart, F., Joachimiak, A., Stevens, R.C., Kuhn, P., Kossiakoff, A., Ismagilov, R.F.

(2006) Angew Chem Int Ed Engl 45: 8156-8160

PubMed: 17099920 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.200602946
Primary Citation Related Structures:
2H1J, 2H1N

Organizational Affiliation

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 5735 S. Ellis Avenue Chicago, IL 60615, USA.

Macromolecule Content

Total Structure Weight: 134.12 kDa
Atom Count: 9,341
Modeled Residue Count: 1,129
Deposited Residue Count: 1,134
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoendopeptidase F	A, B	567	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: GK0963 EC: 3.4.24
UniProt
Find proteins for Q5L1D2 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L1D2 Go to UniProtKB: Q5L1D2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5L1D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-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: 3.10 Å
R-Value Free: 0.225 (Depositor), 0.223 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.324	α = 90
b = 119.324	β = 90
c = 248.736	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-06-13

Deposition Author(s):

Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

Revision History (Full details and data files)

Version 1.0: 2006-06-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary