1TZZ | pdb_00001tzz

Crystal structure of the protein L1841, unknown member of enolase superfamily from Bradyrhizobium japonicum

PDB DOI: https://doi.org/10.2210/pdb1TZZ/pdb

Classification: structural genomics, unknown function
Organism(s): Bradyrhizobium japonicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-07-12 Released: 2004-10-05
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Yew, W.S., Gerlt, J.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1TZZ

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

Literature

Crystal structure of the protein L1841, unknown member of enolase superfamily from Bradyrhizobium japonicum

Fedorov, A.A., Fedorov, E.V., Yew, W.S., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 86.84 kDa
Atom Count: 6,155
Modeled Residue Count: 753
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein L1841	A, B	392	Bradyrhizobium japonicum	Mutation(s): 0 EC: 4.2.1.81
UniProt
Find proteins for Q89FH0 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89FH0 Go to UniProtKB: Q89FH0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89FH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.254 (Depositor), 0.254 (DCC)
R-Value Work: 0.234 (Depositor), 0.235 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.975	α = 90
b = 178.003	β = 90
c = 110.519	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-10-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references

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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.