3BDE

Crystal structure of a dabb family protein with a ferredoxin-like fold (mll5499) from mesorhizobium loti maff303099 at 1.79 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BDE/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Mesorhizobium japonicum MAFF 303099
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-14 Released: 2007-11-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of domain of unknown function with a ferredoxin-like fold (NP_106155.1) from Mesorhizobium loti at 1.79 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 29.68 kDa
Atom Count: 1,989
Modelled Residue Count: 199
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mll5499 protein	A, B	120	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0 Gene Names: NP_106155.1, mll5499
UniProt
Find proteins for Q98BN1 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98BN1 Go to UniProtKB: Q98BN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q98BN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 1.79 Å
R-Value Free: 0.224
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M33BDE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.669	α = 90
b = 28.415	β = 117.78
c = 76.985	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
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-27
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

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Help and Resources

3BDE

Crystal structure of a dabb family protein with a ferredoxin-like fold (mll5499) from mesorhizobium loti maff303099 at 1.79 A resolution

Crystal structure of domain of unknown function with a ferredoxin-like fold (NP_106155.1) from Mesorhizobium loti at 1.79 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)