3BB5 | pdb_00003bb5

CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN OF UNKNOWN FUNCTION (JANN_3925) FROM JANNASCHIA SP. CCS1 AT 2.30 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3BB5/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Jannaschia sp. CCS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-09 Released: 2007-11-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of dimeric ferredoxin-like protein of unknown function (YP_511867.1) from Jannaschia sp. CCS1 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 84.65 kDa
Atom Count: 5,027
Modeled Residue Count: 624
Deposited Residue Count: 726
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stress responsive alpha-beta protein	A, B, C, D, E A, B, C, D, E, F	121	Jannaschia sp. CCS1	Mutation(s): 0 Gene Names: YP_511867.1, Jann_3925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain M [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	H [auth B], J [auth C], K [auth D], M [auth E], O [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain I [auth C] SDF format, chain G [auth A] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A]	G [auth A], I [auth C], L [auth E], N [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Focus chain L [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth C] Focus chain L [auth E] Focus chain N [auth F]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.222 (Depositor), 0.220 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BB5

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.721	α = 90
b = 66.323	β = 93.41
c = 110.452	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, 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: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary