5LFM | pdb_00005lfm

MamA RS-1 ArsTM double mutant

PDB DOI: https://doi.org/10.2210/pdb5LFM/pdb

Classification: PROTEIN BINDING
Organism(s): Solidesulfovibrio magneticus RS-1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-07-03 Released: 2017-08-02
Deposition Author(s): Zarivach, R., Cronin, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free:
0.188 (Depositor), 0.191 (DCC)
R-Value Work:
0.171 (Depositor), 0.175 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Differing self-assembling protein nanostructures in soluble and crystal form reveal dynamic behaviour

Cronin, S.L., Navon, Y., Zarivach, R., Bitton, R.

To be published.

Macromolecule Content

Total Structure Weight: 139.95 kDa
Atom Count: 8,563
Modeled Residue Count: 1,060
Deposited Residue Count: 1,212
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnetosome protein MamA	A, B, C, D, E A, B, C, D, E, F	202	Solidesulfovibrio magneticus RS-1	Mutation(s): 0 Gene Names: mamA, DMR_41160
UniProt
Find proteins for C4XPQ7 (Solidesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)) Explore C4XPQ7 Go to UniProtKB: C4XPQ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4XPQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free: 0.188 (Depositor), 0.191 (DCC)
R-Value Work: 0.171 (Depositor), 0.175 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.122	α = 90
b = 150.122	β = 90
c = 203.947	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Zarivach, R.

Cronin, S.L.

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Refinement description

5LFM | pdb_00005lfm

MamA RS-1 ArsTM double mutant

Literature

Differing self-assembling protein nanostructures in soluble and crystal form reveal dynamic behaviour

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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