3HL1 | pdb_00003hl1

CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULOBACTER VIBRIOIDES AT 1.95 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3HL1/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Caulobacter vibrioides
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-26 Released: 2009-06-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HL1

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

Literature

Crystal structure of ferritin like protein from Caulobacter crescentus CB15 (NP_419375.1) from Caulobacter crescentus at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 70.96 kDa
Atom Count: 4,736
Modeled Residue Count: 571
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin like protein	A, B	317	Caulobacter vibrioides	Mutation(s): 0 Gene Names: CC_0557, NP_419375.1
UniProt
Find proteins for Q9AAP0 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9AAP0 Go to UniProtKB: Q9AAP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9AAP0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	C [auth A], D [auth B]	Unknown ligand		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: 1.95 Å
R-Value Free: 0.232 (Depositor), 0.234 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.633	α = 90
b = 44.017	β = 96.17
c = 119.381	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary

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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.